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Hammack B, Attfield K, Clayton D, Dec E, Dong A, Sarisky C, Bowler BE. The magnitude of changes in guanidine-HCl unfolding m-values in the protein, iso-1-cytochrome c, depends upon the substructure containing the mutation. Protein Sci 1998; 7:1789-95. [PMID: 10082376 PMCID: PMC2144081 DOI: 10.1002/pro.5560070814] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hydrophilic to hydrophobic mutations have been made at 11 solvent exposed sites on the surface of iso-1-cytochrome c. Most of these mutations involve the replacement of lysine with methionine, which is nearly isosteric with lysine. Minimal perturbation to the native structure is expected, and this expectation is confirmed by infrared amide I spectroscopy. Guanidine hydrochloride denaturation studies demonstrate that these variants affect the magnitude of the m-value, the rate of change of free energy with respect to denaturant concentration, to different degrees. Changes in m-values are indicative of changes in the equilibrium folding mechanism of a protein. Decreases in m-values are normally thought to result either from an increased population of intermediates during unfolding or from a more compact denatured state. When cytochrome c is considered in terms of its thermodynamic substructures, the changes in the m-value for a given variant appear to depend upon the substructure in which the mutation is made. These data indicate that the relative stabilities and physical properties of substructures of cytochrome c play an important determining role in the equilibrium folding mechanism of this protein.
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Affiliation(s)
- B Hammack
- Department of Chemistry and Biochemistry, University of Denver, Colorado 80208, USA
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52
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Dong A, Matsuura J, Manning MC, Carpenter JF. Intermolecular beta-sheet results from trifluoroethanol-induced nonnative alpha-helical structure in beta-sheet predominant proteins: infrared and circular dichroism spectroscopic study. Arch Biochem Biophys 1998; 355:275-81. [PMID: 9675038 DOI: 10.1006/abbi.1998.0718] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
2,2,2-Trifluoroethanol (TFE)-induced nonnative alpha-helical structure in peptides and proteins has been extensively studied with circular dichroism (CD) spectroscopy. However, to date, complementary information from infrared (IR) spectroscopy has not been reported. Using both IR and CD spectroscopy, we demonstrate here that the TFE-induced nonnative alpha-helical structure in two beta-sheet-predominant proteins, beta-lactoglobulin and alpha-chymotrypsin, is unstable in comparison with those found in the alpha-helix-predominant proteins myoglobin and cytochrome c under identical conditions. IR spectra showed that, immediately after dissolution of the beta-sheet proteins in 50% (v/v) TFE, a strong amide I band component appears at 1654 cm-1 in H2O and at 1650 cm-1 in D2O, which is ascribed to alpha-helical structure. However, the intensities of the alpha-helical bands decrease as a function of time, concomitant with the appearance of two new band components near 1620 and 1695 cm-1 in H2O and 1612 and 1684 cm-1 in D2O, a typical IR spectral pattern for an intermolecular beta-sheet aggregate. Clear gels begin to develop within 30 min. No similar spectral changes were observed for the alpha-helical proteins. CD spectra suggested initially that the TFE-induced alpha-helix was retained in the gelled state. However, further analysis of the spectra, and Gaussian function modeling with basic spectra, indicated that the apparent alpha-helix signal was actually due to a combination of signals from intermolecular beta-sheet and residual alpha-helix. These results indicate that the TFE-induced nonnative alpha-helix structure in predominantly beta-sheet proteins is unstable and readily converts to an intermolecular beta-sheet aggregate.
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Affiliation(s)
- A Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, Colorado, 80639, USA
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53
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Affiliation(s)
- J F Carpenter
- University of Colorado, Center for Pharmaceutical Biotechnology, Denver 80262, USA.
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54
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Dong A, Kendrick B, Kreilgârd L, Matsuura J, Manning MC, Carpenter JF. Spectroscopic study of secondary structure and thermal denaturation of recombinant human factor XIII in aqueous solution. Arch Biochem Biophys 1997; 347:213-20. [PMID: 9367527 DOI: 10.1006/abbi.1997.0349] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The secondary structure and thermal denaturation (in H2O vs D2O) of recombinant human factor XIII in aqueous solutions were investigated using infrared and circular dichroism (CD) spectroscopies. The infrared amide I spectrum of the protein in H2O solution at 25 degrees C exhibited an absorbance maximum near 1642 cm-1, indicating the presence of a predominantly beta-sheet structure. Quantitative analysis revealed that the native protein contains 13-16% alpha-helix, 41-49% beta-sheet, 29% beta-turn, and 10-14% extended strand structures. The presence of a strong low-wavenumber beta-sheet band at 1641 cm-1 and a weak high-wavenumber beta-sheet band at 1689 cm-1 indicated that the beta-sheet structure of the protein is predominantly antiparallel. Quantitative analysis of the CD spectrum using the SELCON method indicated a secondary structural content of 10% alpha-helix, 40-50% beta-sheet, 20-35% beta-turns, and 20-35% unordered elements, which matches that determined by X-ray crystallography. The apparent discrepancy with the contents of unordered element determined by infrared spectroscopy is reconciled by considering that CD spectroscopy and X-ray crystallography assign extended loops and strands to unordered elements, whereas infrared spectroscopy recognizes these as distinct structured elements. During heating above 60 degrees C, a pair of new infrared bands appeared at 1626 and 1693 cm-1 for the protein in H2O and 1619 and 1683 cm-1 in D2O, indicating a formation of intermolecular beta-sheet aggregates. The intensities of the new bands increased as a function of temperature, concomitant with an intensity decrease in bands for the native protein structural elements. As expected, there was an increase in thermal stability in D2O relative to that in H2O, which was manifested as an increase of about 5 degrees C in the temperature for initial loss of infrared bands assigned to native structural elements and for appearance of bands due to intermolecular beta-sheet. In addition, the midpoint of the thermally induced transitions in infrared spectra were about 2.5 degrees C higher in D2O than in H2O. Based on the infrared analysis, the thermally denatured state of the protein in both H2O and D2O contains predominantly intermolecular beta-sheet. The broad, poorly resolved absorbance that spans the region between the intermolecular beta-sheet bands was assigned to an ensemble of heterogeneous structural elements (including unordered), none of which is populated to a high enough degree to result in a distinct infrared band. Results from CD spectroscopy support these conclusions about the structure of the denatured, aggregated protein.
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Affiliation(s)
- A Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, Colorado 80639, USA
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55
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Calvert JF, Hill JL, Dong A. Redox-dependent conformational changes are common structural features of cytochrome c from various species. Arch Biochem Biophys 1997; 346:287-93. [PMID: 9343376 DOI: 10.1006/abbi.1997.0324] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Discrepant results from X-ray crystallographic and physicochemical studies on the conformations of the two redox states of cytochrome c raise important questions about the nature of redox-dependent conformational changes and whether differences are common structural features of various cytochrome c species. Comparative studies of cytochrome c from 10 species (horse, cow, sheep, pig, dog, rabbit, chicken, pigeon, tuna, and baker's yeast) in aqueous solutions were carried out using Fourier transform infrared (FT-IR) spectroscopy. The second-derivative analysis revealed similar conformational changes in all 10 species upon reduction of the heme iron regardless of the differences in the amino acid sequences. The redox-dependent changes involve the amide I regions ascribed to extended beta-structure, beta-turn, and alpha-helix structures. Three species (cow, sheep, and pig) with identical amino acid sequences displayed nearly identical infrared spectra for the oxidized and reduced states, which rules out the possible contribution of experimental error. These results show unequivocally that redox-dependent conformational changes are common structural feature of various cytochrome c species and demonstrate the usefulness of FT-IR spectroscopy as a quick and inexpensive tool in comparative studies of functionally related conformational changes of proteins.
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Affiliation(s)
- J F Calvert
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley 80639, USA
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56
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Abstract
Sustained delivery systems can achieve more constant blood levels of protein therapeutics than those obtained with bolus doses, leading to improved drug efficacy and fewer adverse side effects. Several different polymeric delivery systems have been studied, including poloxamers, which are unique because they can be prepared in aqueous buffers that are compatible with proteins. Poloxamers are nontoxic block copolymers of poly(ethylene oxide) and poly(propylene oxide). Certain poloxamers exhibit reversible thermal gelation. Thus, a solution of protein and poloxamer prepared at low temperatures and injected extravascularly will form a gel as it warms to body temperature. Subsequently, the protein is released slowly from the gel. To date, however, poloxamer gel delivery systems have been limited to relatively low protein concentrations (i.e., < or = 0.4 mg/mL) that produce a completely soluble protein and an optically clear gel. Much higher concentrations of other protein drugs might be needed to obtain an efficacious sustained dose. In the current in vitro study we found that a poloxamer 407 (22% wt/wt) matrix could be prepared containing tens of milligrams/mililiter of the model proteins alpha-chymotrypsin and lactate dehydrogenase. Under these conditions the protein forms a homogeneous suspension. Warming through the poloxamer 407 transition temperature (ca. 18 degrees C) results in a gel that retains a homogeneous distribution of protein precipitates for several days at 37 degrees C. Infrared spectroscopy documented that the precipitated proteins in the suspension have native secondary structure. Furthermore, the fully active protein can be recovered completely when the gel is dissolved in excess buffer. Finally, at the higher protein concentrations used to form the suspensions in poloxamer 407, protein stability during incubation at 37 degrees C was greatly improved over that seen at lower protein concentrations.
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Affiliation(s)
- L P Stratton
- University of Colorado Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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57
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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58
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Hu K, Dong A, Yao X, Kobayashi H, Iwasaki S. Antineoplastic agents. II. Four furostanol glycosides from rhizomes of Dioscorea collettii var. hypoglauca. Planta Med 1997; 63:161-5. [PMID: 17252340 DOI: 10.1055/s-2006-957636] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
During activity-guided fractionations to screen for antineoplastic agents, further studies by means of preparative HPLC led to the isolation of four known furostanol saponins: protoneodioscin, protodioscin, protoneogracillin, protogracillin, along with their corresponding artifacts: methyl protoneodioscin, methyl protodioscin, methyl protoneogracillin, and methyl protogracillin, from the rhizomes of Dioscorea collettii var. hypoglauca. Among them, protoneodioscin, protodioscin, and protoneogracillin are first reported from the title plant. The structures of the compounds were established on the basis of chemical evidence and spectral analysis (1H-NMR, 13C-IMMR, 1H-1H COSY, HMQC, HMBC, and FAB-MS). These eight compounds all caused morphological abnormality of Pyricularia oryzae mycelia. They also showed cytotoxic activities against the cancer cell line of K562 in vitro as antineoplastic agents.
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Affiliation(s)
- K Hu
- Department of Phytochemistry, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110015, People's Republic of China
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59
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Godbole S, Dong A, Garbin K, Bowler BE. A lysine 73-->histidine variant of yeast iso-1-cytochrome c: evidence for a native-like intermediate in the unfolding pathway and implications for m value effects. Biochemistry 1997; 36:119-26. [PMID: 8993325 DOI: 10.1021/bi961915m] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this paper we report thermodynamic studies on a variant of yeast iso-1-cytochrome c in which a surface lysine residue at position 73 has been replaced with a histidine (H73). Guanidine hydrochloride denaturation studies monitored by circular dichroism spectroscopy indicated decreased thermodynamic stability (a lower delta G(o)(u)H20) and a smaller m value for the H73 protein as compared to the wild type (WT) protein. Further investigations to probe the causes for the thermodynamic stability differences between the two proteins involved guanidine hydrochloride and urea denaturations monitored by tryptophan fluorescence. The stability of heme ligation in the denatured state in the presence of either guanidine hydrochloride or urea was monitored by the spin-state transition of the heme iron induced by pH. None of these studies supported the hypothesis that the decreased m value was due to heme-His73 ligation in the denatured state. Guanidine hydrochloride denaturations monitored by the change in the extinction coefficient at 695 nm, which is sensitive to the presence of heme-Met80 ligation, revealed a native-like intermediate for the H73 protein, probably caused by displacement of the Met80 heme ligand by histidine 73 at guanidine hydrochloride concentrations much lower than required for full cooperative unfolding. Presence of the native-like intermediate is most likely the cause of the smaller m value and decreased thermodynamic stability for the CD-monitored H73 protein unfolding as compared to the unfolding of the WT protein. Guanidine hydrochloride denaturations in the presence of 200 mM imidazole provide further evidence in support of the proposed mechanism.
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Affiliation(s)
- S Godbole
- Department of Chemistry and Biochemistry, University of Denver, Colorado 80208, USA
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60
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Hu K, Dong A, Yao X, Kobayashi H, Iwasaki S. Antineoplastic agents; I. Three spirostanol glycosides from rhizomes of Dioscorea collettii var. hypoglauca. Planta Med 1996; 62:573-575. [PMID: 9000889 DOI: 10.1055/s-2006-957978] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
By activity-guided fractionation, three known steroidal saponins, prosapogenin A of dioscin, dioscin and gracillin, were isolated from the total saponin fraction of Dioscorea coiletti var. hypoglauca as active compounds causing morphological abnormality of Pyricularia oryzae mycelia. The compounds also exhibited cytotoxic activity against the cancer cell line K562 in vitro. The structures of the compounds were elucidated on the basis of chemical evidence and IR, FAB-MS, 1H-NMR, 13C-NMR, and two-dimensional NMR (2D-NMR) analysis.
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Affiliation(s)
- K Hu
- Department of Phytochemistry, Shenyang Pharmaceutical University, People's Republic of China
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61
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Chang BS, Beauvais RM, Arakawa T, Narhi LO, Dong A, Aparisio DI, Carpenter JF. Formation of an active dimer during storage of interleukin-1 receptor antagonist in aqueous solution. Biophys J 1996; 71:3399-406. [PMID: 8968609 PMCID: PMC1233827 DOI: 10.1016/s0006-3495(96)79534-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The degradation products of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) formed during storage at 30 degrees C in aqueous solution were characterized. Cationic exchange chromatography of the stored sample showed two major, new peaks eluting before (P1) and after (L2) the native protein, which were interconvertible. Size-exclusion chromatography and electrophoresis documented that both the P1 and L2 fractions were irreversible dimers, formed by noncovalent interactions. A competition assay with interleukin-1 indicated that on a per monomer basis the P1 and L2 dimers retained about two-thirds of the activity of the native monomer. Infrared and far-UV circular dichroism spectroscopies showed that only minor alterations in secondary structure arose upon the formation of the P1 dimer. However, alteration in the near-UV circular dichroism spectrum suggested the presence of disulfide bonds in the P1 dimer, which are absent in the native protein. Mass spectroscopy and tryptic mapping, before and after carboxymethylation, demonstrated that the P1 dimer contained an intramolecular disulfide bond between Cys-66 and Cys-69. Although conversion of native protein to the P1 dimer was irreversible in buffer alone, the native monomer could be regained by denaturing the P1 dimer with guanidine hydrochloride and renaturing it by dialysis, suggesting that the intramolecular disulfide bond does not interfere with refolding. Analysis of the time course of P1 formation during storage at 30 degrees C indicated that the process followed first-order, and not second-order, kinetics, suggesting that the rate-limiting step was not dimerization. It is proposed that a conformational change in the monomer is the rate-limiting step in the formation of the P1 dimer degradation product. Sucrose stabilized the native monomer against this process. This result can be explained by the general stabilization mechanism for this additive, which is due to its preferential exclusion from the protein surface.
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Affiliation(s)
- B S Chang
- Department of Pharmaceutics, Amgen Inc., Thousand Oaks, California 91320-1789, USA.
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62
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Dong A, Meyer JD, Kendrick BS, Manning MC, Carpenter JF. Effect of secondary structure on the activity of enzymes suspended in organic solvents. Arch Biochem Biophys 1996; 334:406-14. [PMID: 8900418 DOI: 10.1006/abbi.1996.0472] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite the extensive use and study of enzymes suspended in organic solvents, whether activity differences between different preparations can be accounted for by differences in protein secondary structure is still unknown. To address this issue, in the current study two model enzymes, alpha-chymotrypsin and subtilisin Carlsberg, were lyophilized and suspended in both polar and nonpolar organic solvents. The secondary structures of the proteins in the initial aqueous solution, in the lyophilized powder, and in the subsequent suspensions in organic solvents were determined using infrared spectroscopy. Lyophilization perturbed the secondary structure of both enzymes. With alpha-chymotrypsin, lyophilization from buffer followed by suspension in ethanol, hexane, or pyridine did not alter the unfolded structure observed in the dried powder. In contrast, with subtilisin Carlsberg, suspension of the dried enzyme in ethanol led to further perturbation of structure, whereas in hexane, and more so in pyridine, there was some return toward native structure. Lyophilization of the aqueous protein solutions in the presence of either trehalose or sorbitol led to retention of more native-like structure of both enzymes in the dried solid. However, large structural perturbations arose when these samples were suspended in organic solvents. The only exception was the subtilisin-trehalose mixture, which regained some native structure in ethanol and hexane. The greatest changes were noted in samples suspended in pyridine, in which the infrared spectra indicated extensive intermolecular beta-sheet formation from protein aggregates. There was not any consistent correlation between activity in organic solvents and either the initial structure obtained in the dried powders or the final structure when suspended in organic solvents. Nor could differences in residual water contents in dried samples or the total water content in the organic solvent reaction system account for the activity differences.
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Affiliation(s)
- A Dong
- Cooperative Program in Pharmaceutical Biotechnology, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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63
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Allison SD, Dong A, Carpenter JF. Counteracting effects of thiocyanate and sucrose on chymotrypsinogen secondary structure and aggregation during freezing, drying, and rehydration. Biophys J 1996; 71:2022-32. [PMID: 8889176 PMCID: PMC1233668 DOI: 10.1016/s0006-3495(96)79400-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Studies of numerous proteins with infrared spectroscopy have documented that unfolding is a general response of unprotected proteins to freeze-drying. Some proteins that are unfolded in the dried solid aggregate during rehydration, whereas others refold. It has been proposed for the latter case that aggregation is avoided because refolding kinetically outcompetes intermolecular interactions. In contrast, with proteins that normally aggregate after rehydration, minimizing unfolding during freeze-drying with stabilizer has been shown to be needed to favor the recovery of native protein molecules after rehydration. The purpose of the current study was to examine first the opposite situation, in which a denaturant is used to foster additional unfolding in the protein population during freeze-drying. If the protein is not intrinsically resistant to aggregation under the study conditions (e.g., because of intermolecular charge repulsion) and the denaturant does not disrupt intermolecular interactions during rehydration, this treatment should favor aggregation upon rehydration. With infrared spectroscopy we found that at concentrations of the denaturant Na thiocyanate (NaSCN) that only slightly perturbed chymotrypsinogen secondary structure in solution before freeze-drying, there was a large increase in protein unfolding in the dried solid and in protein aggregation measured after rehydration. Bands assigned to intermolecular beta sheet were present in the spectra of samples dried with NaSCN, indicating that aggregation could also arise in the dried solid. By examining the protein structure in the frozen state, we determined that in the absence of NaSCN the protein remains native. NaSCN caused structural perturbations during freezing, without the formation of intermolecular beta sheet, that were intermediate to structural changes noted after freeze-drying. In contrast, samples treated in the presence of NaSCN and sucrose had native-like spectra in the frozen and dried states, and much reduced aggregation after rehydration. These results indicate that during freezing and drying the sugar can counteract and mostly reverse the structural perturbations induced by NaSCN before and during these treatments.
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Affiliation(s)
- S D Allison
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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64
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Dong A, Hyslop RM, Pringle DL. Differences in conformational dynamics of ribonucleases A and S as observed by infrared spectroscopy and hydrogen-deuterium exchange. Arch Biochem Biophys 1996; 333:275-81. [PMID: 8806781 DOI: 10.1006/abbi.1996.0391] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Differences in conformational dynamics of bovine pancreatic RNase A and RNase S have been investigated using hydrogen-deuterium (H-D) exchange in conjunction with Fourier transform infrared spectroscopy. Deuteration-induced spectral changes in the amide I and II regions were monitored as a function of time. Second-derivative analysis revealed similar amide I spectral patterns for both proteins in H2O as well as fully deuterated in D2O. However, the rate of amide proton exchange of RNase S is much faster than that of RNase A at 25 degrees C as determined by changes in the intensity ratio of amide II/amide I bands and frequency red-shifts of amide I components. The frequency red-shifts of the amide I components ascribed to beta-sheet, alpha-helix, and beta-turns are continuous as a function of time, indicating that both proteins are too small to contain isolated secondary structural groups containing only exchanged or unexchanged amide protons in the partially deuterated intermediate states. Despite the dramatic difference in H-D exchange rate, the patterns of spectral changes in the conformation-sensitive amide I regions of RNase A and RNase S are very similar throughout the course of deuteration, indicating a similar pathway of amide proton exchange in both proteins.
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Affiliation(s)
- A Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley 80639, USA
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65
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Chang BS, Beauvais RM, Dong A, Carpenter JF. Physical factors affecting the storage stability of freeze-dried interleukin-1 receptor antagonist: glass transition and protein conformation. Arch Biochem Biophys 1996; 331:249-58. [PMID: 8660705 DOI: 10.1006/abbi.1996.0305] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The effects of glass transition of, and protein conformation in, the dried solid on the storage stability of freeze-dried recombinant human interleukin-1 receptor antagonist (rhIL-1ra) were examined. Glass transition is a temperature-dependent phenomenon. Amorphous materials become hard and brittle at temperatures below their characteristic glass transition temperatures (Tg) such that diffusion of molecules along the matrix is not sufficient to cause large-scale structural changes. To ascertain the importance of the glass transition in protein storage stability, we compared 10 different lyophilized rhIL-1ra formulations, with Tgs ranging from 20 to 56 degrees C, during several weeks of storage at temperatures above and below the samples' Tgs. Protein degradation, both deamidation and aggregation, was greatly accelerated at temperatures above Tg, but for some formulations also arose below Tg. Thus, storage of dried proteins below the Tg is necessary but not sufficient to ensure long-term stability. To examine the effects of protein structure in the dried solid, we prepared formulations with various sucrose concentrations, all of which had a Tg = 66 +/- 2.5 degrees C. With infrared spectroscopy, we determined that the protein lyophilized with </=1% sucrose was unfolded in the initial dried solid. In contrast, in those formulations with >/=5% sucrose, conformational change was inhibited during lyophilization. When stored at 50 degrees C, degradation of the freeze-dried protein varied inversely with sucrose concentration. These results indicate that structural changes arising during the lyophilization process led to damage during subsequent storage, even if the storage temperature was less than the Tg. Together the results of these studies document that to obtain optimum stability of dried rhIL-1ra it was necessary to inhibit conformational change during lyophilization and to store at temperatures below the Tg of the dried formulation.
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Affiliation(s)
- B S Chang
- Department of Pharmaceutics and Drug Delivery, Amgen, Inc., Amgen Center MS 8-1-A, Thousand Oaks, California, 91320, USA
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66
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Dong A, Matsuura J, Allison SD, Chrisman E, Manning MC, Carpenter JF. Infrared and circular dichroism spectroscopic characterization of structural differences between beta-lactoglobulin A and B. Biochemistry 1996; 35:1450-7. [PMID: 8634275 DOI: 10.1021/bi9518104] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Structural differences between two genetic variants of bovine beta-lactoglobulins (type A and B) in aqueous solutions were characterized using Fourier transform infrared and circular dichroism spectroscopies. To probe differences in structural dynamics, the effects hydrogen-deuterium exchange were also compared for the two proteins. The infrared spectra recorded in H2O solution for the two proteins were nearly identical in the conformationlly sensitive amide I region. The only exceptions were small differences at the band ascribed to a high-wavenumber beta-sheet component near 1693 cm-1 and the band assigned to turns at 1684 cm-1. In contrast, when the proteins were prepared in D2O solution, marked spectral differences were observed at all regions ascribed to beta-sheet and turn structures. These differences are consistent with the structural differences of the two variants at amino acid residues 64 and 118, which are located at a turn and a beta-sheet structure, respectively, as revealed by X-ray crystallographic studies [Monaco et al. (1987) J. Mol. Biol. 197, 695-706]. The circular dichroism spectra for the two proteins were essentially identical, both before and after hydrogen-deuterium exchange. Therefore, hydrogen-deuterium exchange did not alter the proteins' secondary structure. The enhancement of the amide I spectral difference upon hydrogen-deuterium exchange was ascribed to the differences in the structural mobility of the two proteins. Since the rate of exchange was greater for variant A, it was concluded that this variant has greater structural mobility than variant B. These findings indicate that the combination of infrared spectroscopy and hydrogen-deuterium exchange has great potential in characterization of even subtle structural differences in proteins induced by naturally occurring point mutations and/or site-directed mutagenesis.
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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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Kendrick BS, Dong A, Allison SD, Manning MC, Carpenter JF. Quantitation of the area of overlap between second-derivative amide I infrared spectra to determine the structural similarity of a protein in different states. J Pharm Sci 1996; 85:155-8. [PMID: 8683440 DOI: 10.1021/js950332f] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Maintaining a native-like structure of protein pharmaceuticals during lyophilization is an important aspect of formulation. Infrared spectroscopy can be used to evaluate the effectiveness of formulations in protecting the secondary structural integrity of proteins in the dried solid. This necessitates making quantitative comparisons of the overall similarity of infrared spectra in the conformationally sensitive amide I region. We initially used the correlation coefficient r, as defined by Prestrelski et al. (Biophys. J. 1993, 65, 661-671), for this quantitation. Occasionally, we noticed that the r value did not agree with a visual assessment of the spectral similarity. In some cases this was due to an offset in baselines, which led artifactually to an unreasonably low r value. Conversely, if the spectra were baseline corrected and there existed a large similarity between peak positions, but differences in relative peak heights, the r value would be unreasonably high. Our approach to avoiding these problems is to use area-normalized second-derivative spectra. We have found that quantitating the area of overlap between area-normalized spectra provides a reliable, objective method to compare overall spectral similarity. In the current report, we demonstrate this method with selected protein spectra, which were taken from experiments where unfolding was induced by lyophilization or guanidine hydrochloride, and artificial data sets. With this analysis, we document how problems associated with calculation of the correlation coefficient, r, are avoided.
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Affiliation(s)
- B S Kendrick
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver 80262, USA
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68
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Dong A, Huang P, Caughey WS. Redox-dependent changes in beta-sheet and loop structures of Cu,Zn superoxide dismutase in solution observed by infrared spectroscopy. Arch Biochem Biophys 1995; 320:59-64. [PMID: 7793985 DOI: 10.1006/abbi.1995.1342] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Redox-dependent conformational changes of bovine Cu,Zn superoxide dismutase in 20 mM phosphate buffer (pH 7.4) were studied at 20 degrees C using Fourier transform infrared spectroscopy. Amide I spectra provide evidence that conformational changes in the protein accompany a change in the oxidation state of copper at the active site. Quantitative analysis of these spectra indicates that both reduced (CuI,ZnII) and oxidized (CuII,ZnII) enzymes are composed of about 35% antiparallel beta-sheet, 45% unordered/loop, and 20% beta-turn structures. Significant redox-dependent changes occur in regions ascribed to beta-sheet and unordered/loop structures that are consistent with an active channel structure wherein the copper ion bonds to imidazolate side chains of His 44, 46, and 118 within the beta-sheet structure and also to the imidazolate side chain of His 61 associated with unordered/loop structure. This study provides the first experimental evidence that an unordered structure can exhibit bands in more than one region, one near 1658 cm-1 and another near 1648 cm-1 in both H2O and D2O solutions. The detected changes in protein conformation are expected to be critical to the catalytic function of this enzyme.
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523, USA
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69
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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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70
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Huang P, Dong A, Caughey WS. Effects of dimethyl sulfoxide, glycerol, and ethylene glycol on secondary structures of cytochrome c and lysozyme as observed by infrared spectroscopy. J Pharm Sci 1995; 84:387-92. [PMID: 7629725 DOI: 10.1002/jps.2600840402] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Effects of 10-30% (v/v) of dimethyl sulfoxide, glycerol, and ethylene glycol on the H-O-H bending vibration of water and the amide I bands of horse heart cytochrome c and chicken egg white lysozyme in 25 mM sodium phosphate buffer (pH 7.4) were examined at 20 degrees C by Fourier transform infrared spectroscopy. The H-O-H bending mode of water was strongly affected by these cryoprotectant solvents. Increasing the concentration of cryosolvents from 0 to 30% shifts the water bending band maximum from 1645 to about 1650 cm-1. Second-derivative analysis reveals significant changes in conformation-sensitive amide I regions of lysozyme ascribed to alpha-helix (1657 cm-1), turn (1674 cm-1), and unordered (1646 cm-1) structures; each cryosolvent increases the intensity of the 1657 cm-1 band at the expense of bands at 1674 and 1646 cm-1. No changes in spectra deemed significant were observed for cytochrome c under the same conditions. There is no spectral evidence of structural randomization of proteins due to the presence of these cryosolvents. Cryosolvent-induced changes in secondary structure of proteins may result from changes in water structure which, in turn, perturb the structure of the protein and/or from direct interactions between cryosolvent and protein.
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Affiliation(s)
- P Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523, USA
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71
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Abstract
Snake venoms, especially from the Crotalidae family, contain a variety of enzymes that prevent blood coagulation by virtue of their fibrinolytic enzymes. Nineteen snake venoms were screened for fibrinolytic activity and the highest activity was found in the venom of Crotalus basiliscus basiliscus venom. The active principle, basilase, was isolated, purified, and found to have fibrinolytic and fibrinogenolytic activity. It had a molecular weight of 22,000 and 1 mol of zinc per mole of protein associated with it. The proteolytic activity of the enzyme against dimethyl casein was inhibited by ethylenediaminetetraacetic acid and alpha 2-macroglobulin. It did not inactivate alpha 2-macroglobulin. Basilase did not have any of the following activities: thrombin-like, factor X-like, protein C activating, or urokinase-like. It caused neither hemorrhage nor platelet aggregation. In spite of its proteolytic activity, basilase did not hydrolyze the membranes of platelets. Basilase had 24% alpha-helix, 31% beta-sheet, 25% turns, and 20% unordered structure, as determined by Fourier Transform Infrared spectroscopy. Basilase is an enzyme that hydrolyzes fibrin directly without activation of plasminogen.
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Affiliation(s)
- G Datta
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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72
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Herrmann L, Bowler BE, Dong A, Caughey WS. The effects of hydrophilic to hydrophobic surface mutations on the denatured state of iso-1-cytochrome c: investigation of aliphatic residues. Biochemistry 1995; 34:3040-7. [PMID: 7893716 DOI: 10.1021/bi00009a035] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A series of hydrophilic to hydrophobic surface mutations were prepared at the highly solvent-exposed lysine 73 of iso-1-cytochrome c to assess the ability of such mutants to affect the energetics of the denatured state. In this report, the aliphatic hydrophobics (leucine, isoleucine, valine, alanine, glycine) were studied. The thermodynamic stability of each of these mutants was determined by guanidine hydrochloride denaturation. Both the free energy of unfolding in the absence of denaturant, delta GouH2O, and the slope, m, of a plot of the free energy of unfolding, delta Gou, versus [guanidine hydrochloride] show significant negative correlations with the 1-octanol to water transfer free energy, delta Gtr, of the amino acid side chain at position 73. A negative correlation with hydrophobicity is consistent with these mutants leading to more extensive hydrophobic clustering in the denatured state, consistent with the predictions of heteropolymer theory for compact denatured states; an effect operating on the native state energetics should produce a positive correlation of delta GouH2O with hydrophobicity. Infrared amide I spectroscopy indicated native state structural perturbations for the glycine 73 and isoleucine 73 mutants. A moderate correlation of delta GouH2O was also found with alpha-helix propensity, suggesting that both hydrophobic effects acting on the denatured state and alpha-helix propensity are affecting the delta GouH2O values for these mutants.
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Affiliation(s)
- L Herrmann
- Department of Chemistry, University of Denver, Colorado 80208
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73
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Dong A, Huang P, Caughey B, Caughey WS. Infrared analysis of ligand- and oxidation-induced conformational changes in hemoglobins and myoglobins. Arch Biochem Biophys 1995; 316:893-8. [PMID: 7864648 DOI: 10.1006/abbi.1995.1120] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Effects of the binding of O2 and CO to heme iron (II) of deoxy forms and of the oxidation of deoxy forms to aquoiron (III) complexes on the infrared spectra of hemoglobins and myoglobins have been examined. Spectra were measured for aqueous solutions 3-4 mM in heme of human, bovine, and equine hemoglobins and sperm whale, bovine, and equine myoglobins in 10 mM sodium phosphate buffer, pH 7.4, at 20 degrees C. All ligand binding and oxidation reactions resulted in similar spectral shifts in the region 1665 to 1670 cm-1, a portion of the amide I region assignable to beta-turn structure. There were no other significant changes in the amide I region, a finding consistent with no other alterations in secondary structure. The major bands near 1655 cm-1 associated with alpha-helices were consistently at 2 cm-1 lower wavenumber for myoglobins than for hemoglobins. The changes in solution infrared spectra observed in this study may result at least in part from conformational changes at the FG corner associated with movements of F and E helices that have been noted previously in crystal structures.
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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74
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Dong A, Nagai M, Yoneyama Y, Caughey WS. Determination of the amounts and oxidation states of hemoglobins M Boston and M Saskatoon in single erythrocytes by infrared microspectroscopy. J Biol Chem 1994; 269:25365-8. [PMID: 7929232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The reduced abnormal subunits of two M-type hemoglobins, Boston (His alpha 58-->Tyr) and Saskatoon (His beta 63-->Tyr), have been determined in the presence of normal human hemoglobin A by measurement of C-O stretch bands in infrared spectra of carbon monoxide complexes. Use of an infrared microscope coupled to a Fourier transform infrared spectrometer of high sensitivity permitted measurements to be made on as small a hemoglobin mixture as is contained in a single erythrocyte. The abnormal subunits of both Hbs M exhibit bands near 1970 cm-1 compared with bands near 1951 cm-1 for the normal subunits. The increase in 1970 cm-1 band intensity upon erythrocyte reduction with dithionite provided a measure of the extent of abnormal subunit oxidation; in cell suspensions about 60% of the abnormal subunits of Hb M Boston and 80% for Hb M Saskatoon remained reduced. The amount of Hb present as abnormal Hb averaged about 25% for Hb M Boston cells and about 50% for Hb M Saskatoon cells. However, the ratio of Hb M to Hb A in individual cells varied markedly, with the ratio expected to decrease as the cell ages. These results demonstrate the unique utility of infrared microspectroscopy for the study of differences in abnormal Hb status among individual erythrocytes.
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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75
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Dong A, Nagai M, Yoneyama Y, Caughey WS. Determination of the amounts and oxidation states of hemoglobins M Boston and M Saskatoon in single erythrocytes by infrared microspectroscopy. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47257-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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76
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Dong A, Huang P, Zhao XJ, Sampath V, Caughey WS. Characterization of sites occupied by the anesthetic nitrous oxide within proteins by infrared spectroscopy. J Biol Chem 1994; 269:23911-7. [PMID: 7929038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We report here a comprehensive infrared spectroscopic study of the interactions between the anesthetic nitrous oxide (N2O) and six proteins: lysozyme, cytochrome c, myoglobin, hemoglobin, serum albumin, and cytochrome c oxidase. Sites occupied by N2O molecules within these proteins were characterized. Three types of hydrophobic sites were found within the proteins. One with nu 3 near 2225 cm-1 is likely to be near peptide bond carbonyls; one with nu 3 near 2219 cm-1 may be near a benzene-like structure such as the side chains of phenylalanine and tyrosine; and the other with nu 3 near 2215 cm-1 is likely to be in a nonpolar alkane-like environment provided by the side chains of Leu, Ile, and Val residues. The amount of N2O molecules bound to myoglobin increases as the pH decreases from 9.2 to 5.2. N2O-protein interactions produced no detectable changes in the ligand-binding pockets of myoglobin, hemoglobin, and cytochrome c oxidase. N2O-induced secondary structure changes were detected only in the fully reduced cytochrome c oxidase, not in the fully oxidized oxidase and the other five proteins. N2O-induced conformational changes in the alpha beta-interface of hemoglobin and the h2 and h3 alpha-helices of human serum albumin were detected by monitoring the S-H stretch vibrations of cysteine residues. These findings provide direct evidence that anesthetic N2O interacts with proteins and occupies sites in the interior of the proteins.
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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77
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Dong A, Huang P, Zhao X, Sampath V, Caughey W. Characterization of sites occupied by the anesthetic nitrous oxide within proteins by infrared spectroscopy. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(19)51025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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78
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Bowler BE, Dong A, Caughey WS. Characterization of the guanidine hydrochloride-denatured state of iso-1-cytochrome c by infrared spectroscopy. Biochemistry 1994; 33:2402-8. [PMID: 8117700 DOI: 10.1021/bi00175a008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Infrared spectroscopy has been used to monitor residual ordered structure in the denatured state of wild-type and two mutants of iso-1-cytochrome c. The technique used involves a careful digital subtraction procedure that removes spectral contributions from buffer, water vapor, and the denaturant guanidine hydrochloride. Reliable and reproducible spectra can be produced using these methods. The data for iso-1-cytochrome c show upon denaturation a shift of the structure-sensitive amide I infrared band away from the spectral region associated with random structure. Second-derivative resolution enhancement of the amide I absorption band uncovers several bands which can be associated with various residual ordered structures in the denatured state. Gradual changes in the amide I band after denaturation are also observed as the guanidine hydrochloride concentration is increased. Two single-site mutants of iso-1-cytochrome c, which have been shown to have more compact denatured states than the wild-type protein, exhibited denatured-state infrared spectra with significant differences from the wild-type protein spectra. These observations provide new insight into the characteristics of protein denatured states.
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Affiliation(s)
- B E Bowler
- Department of Chemistry, University of Denver, Colorado 80208
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79
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Dong A, Caughey WS, Du Clos TW. Effects of calcium, magnesium, and phosphorylcholine on secondary structures of human C-reactive protein and serum amyloid P component observed by infrared spectroscopy. J Biol Chem 1994; 269:6424-30. [PMID: 8119992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The secondary structures of human C-reactive protein (CRP) and serum amyloid P component (SAP) in D2O-based solutions in the presence or absence of calcium, magnesium, and phosphorylcholine have been investigated using Fourier transform infrared spectroscopy. Quantitative analysis provided estimations of about 50% beta-sheet, 12% alpha-helix, 24% beta-turn, and 14% unordered structure for CRP and about 54% beta-sheet, 12% alpha-helix, 25% beta-turn, and 9% unordered structure for SAP. With both proteins significant calcium-dependent changes were observed in conformation-sensitive amide I regions assigned to each type of structure. The CRP spectrum was also affected by magnesium, but the changes differed from those induced by calcium. The SAP spectrum was not affected by magnesium. Phosphorylcholine in the presence of calcium also affected the spectrum of CRP but not the spectrum of SAP. Our present study provides the first direct comparison of the secondary structures of the pentraxins human CRP and SAP and hamster female protein (Dong, A., Caughey, B., Caughey, W. S., Bhat, K. S., and Coe, J. E. (1992) Biochemistry 32, 9364-9370). These findings suggest that the three pentraxins have similar secondary structure compositions and calcium-dependent conformational changes, but differ significantly in their responses to phosphorylcholine and magnesium. Such properties are expected to be relevant to the incompletely understood roles of these highly conserved proteins including binding to nuclear proteins, complement activation, and association with amyloids.
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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80
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Dong A, Caughey W, Du Clos T. Effects of calcium, magnesium, and phosphorylcholine on secondary structures of human C-reactive protein and serum amyloid P component observed by infrared spectroscopy. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37389-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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81
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Affiliation(s)
- A Dong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523
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82
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Abstract
IR spectra directly probe specific vibrators in bovine heart cytochrome c oxidase, yielding quantitative as well as qualitative information on structures and reactions at these vibrators. C-O IR spectra reveal that CO binds to Fe2+ a3 as two conformers each in isolated immobile environments sensitive to Fea and/or CuA oxidation state but remarkably insensitive to pH, medium, anesthetics, and other factors that affect activity. C-N IR spectra reveal that the one CN- that binds to fully and partially oxidized enzyme can be in three different structures. These structures vary in relative amounts with redox level, thereby reflecting dynamic electron exchange among Fea, CuA, and CuB with associated changes in protein conformation of likely significance in O2 reduction and H(+)-pumping. Azide IR spectra also reflect redox-dependent long-range effects. The amide I IR bands, due to C-O vibrators of peptide linkages and composed of multiple bands derived from different secondary structures, reveal high levels of alpha-helix (approximately 60%) and subtle changes with redox level and exposure to anesthetics. N2O IR spectra reveal that these anesthetic molecules at clinically relevant levels occupy three sites of different polarity within the enzyme as the enzyme is reversibly, but only partially, inhibited.
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Affiliation(s)
- W S Caughey
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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83
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Bowler BE, May K, Zaragoza T, York P, Dong A, Caughey WS. Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: implications for the denatured state. Biochemistry 1993; 32:183-90. [PMID: 8380333 DOI: 10.1021/bi00052a024] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A series of mutations at the highly solvent-exposed lysine 73 of iso-1-cytochrome c have been prepared by site-directed mutagenesis. These mutations were designed to probe denatured-state effects on the unfolding equilibrium of this protein. The hydrophilic amino acid Lys was replaced with the hydrophobic amino acids Met, Tyr, Phe, and Trp. The idea was to induce stabilizing hydrophobic interactions in the unfolded state, while having little effect on the folded-state energy due to the high solvent exposure of this site. Fourier transform infrared spectral analyses indicate that none of these mutations significantly affect the native fold of the protein. The stability of each protein to guanidine hydrochloride denaturation was monitored at 25 degrees C by circular dichroism spectroscopy. All four hydrophobic mutants decreased the value of delta Go uH2O, the free energy of unfolding of the protein in the absence of denaturant, by 1.0-1.5 kcal/mol. The delta Go uH2O values for these proteins correlate linearly (correlation coefficient of 0.98) with the hydrophobicity of the amino acid at position 73 of the sequence. These data are consistent with the idea that the position-73 mutants are more buried in the denatured state than in the native state, suggestive of a compact denatured state where such interactions would be possible.
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Affiliation(s)
- B E Bowler
- Department of Chemistry, University of Denver, Colorado 80208
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84
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Dong A, Caughey B, Caughey WS, Bhat KS, Coe JE. Secondary structure of the pentraxin female protein in water determined by infrared spectroscopy: effects of calcium and phosphorylcholine. Biochemistry 1992; 31:9364-70. [PMID: 1382589 DOI: 10.1021/bi00154a006] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The secondary structure of hamster female protein in aqueous solutions in the presence or absence of calcium and phosphorylcholine has been investigated using Fourier transform infrared spectroscopy. Our present studies provide the first evaluation of the secondary structure of FP and its calcium- and phosphorylcholine-dependent conformational changes. Quantitative analysis indicated that FP is composed of 50% beta-sheet, 11% alpha-helix, 29% beta-turn, and 10% random structures. Calcium- and phosphorylcholine-dependent infrared spectral changes were observed in regions assigned to beta-sheet, alpha-helix, turn, and random structures. The infrared-based secondary structure compositions were used as constraints to compute theoretical locations for the different secondary structures along the amino acid sequence of the FP protein. Two putative calcium-binding sites were proposed for FP (residues 93-109 and 150-168) as well as other members of the pentraxin family on the basis of the theoretical secondary structure predictions and the similarity in sequence between the pentraxins and EF-hand calcium-binding proteins. The changes in protein conformation detected upon binding of calcium and phosphorylcholine provide a mechanism for the effects of these ligands on physiologically important properties of the protein, e.g., activation of complement and association with amyloids.
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Affiliation(s)
- A Dong
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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85
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Abstract
Instrumentation has been developed to automate, accurately guide, and integrate microsurgery laser resection equipment that is used in stereotactic brain surgery. The instrument is a computer-controlled laser-guiding system. The improvement in the accuracy comes from relying on a certain well-referenced three-dimensional surgical orientation, and computer-preplanned tumor contours, rather than only the surgeons hand-eye orientation in the operating room.
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Affiliation(s)
- L Zamorano
- Henry Ford Neurosurgical Institute, Detroit, Mich
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86
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Caughey BW, Dong A, Bhat KS, Ernst D, Hayes SF, Caughey WS. Secondary structure analysis of the scrapie-associated protein PrP 27-30 in water by infrared spectroscopy. Biochemistry 1991; 30:7672-80. [PMID: 1678278 DOI: 10.1021/bi00245a003] [Citation(s) in RCA: 663] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A protease-resistant form of the protein PrP (PrP-res) accumulates in tissues of mammals infected with scrapie, Creutzfeldt-Jakob disease, and related transmissible neurodegenerative diseases. This abnormal form of PrP can aggregate into insoluble amyloid-like fibrils and plaques and has been identified as the major component of brain fractions enriched for scrapie infectivity. Using a recently developed technique in Fourier transform infrared spectroscopy which allows protein conformational analysis in aqueous media, we have studied the secondary structure of the proteinase K resistant core of PrP-res (PrP-res 27-30) as it exists in highly infectious fibril preparations. Second-derivative analysis of the infrared spectra has enabled us to quantitate the relative amounts of different secondary structures in the PrP-res aggregates. The analysis indicated that PrP-res 27-30 is predominantly composed of beta-sheet (47%), which is consistent with its amyloid-like properties. In addition, significant amounts of turn (31%) and alpha-helix (17%) were identified, indicating that amyloid-like fibrils need not be exclusively beta-sheet. The infrared-based secondary structure compositions were then used as constraints to improve the theoretical localization of the secondary structures within PrP-res 27-30.
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Affiliation(s)
- B W Caughey
- NIAID, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana 59840
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87
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Abstract
Infrared spectra have been obtained for 12 globular proteins in aqueous solution at 20 degrees C. The proteins studied, which vary widely in the relative amounts of different secondary structures present, include myoglobin, hemoglobin, immunoglobulin G, concanavalin A, lysozyme, cytochrome c, alpha-chymotrypsin, trypsin, ribonuclease A, alcohol dehydrogenase, beta 2-microglobulin, and human class I major histocompatibility complex antigen A2. Criteria for evaluating how successfully the spectra due to liquid and gaseous water are subtracted from the observed spectrum in the amide I region were developed. Comparisons of second-derivative amide I spectra with available crystal structure data provide both qualitative and quantitative support for assignments of infrared bands to secondary structures. Band frequency assignments assigned to alpha-helix, beta-sheet, unordered, and turn structures are highly consistent among all proteins and agree closely with predictions from theory. alpha-Helix and unordered structures can each be assigned to only one band whereas multiple bands are associated with beta-sheets and turns. These findings demonstrate a method of analysis of second-derivative amide I spectra whereby the frequencies of bands due to different secondary structures can be obtained. Furthermore, the band intensities obtained provide a useful method for estimating the relative amounts of different structures.
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Affiliation(s)
- A Dong
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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88
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Gorga JC, Dong A, Manning MC, Woody RW, Caughey WS, Strominger JL. Comparison of the secondary structures of human class I and class II major histocompatibility complex antigens by Fourier transform infrared and circular dichroism spectroscopy. Proc Natl Acad Sci U S A 1989; 86:2321-5. [PMID: 2928336 PMCID: PMC286904 DOI: 10.1073/pnas.86.7.2321] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have examined the secondary structures of human class I and class II histocompatibility antigens in solution by Fourier transform infrared spectroscopy and circular dichroism in order to compare the relative amounts of alpha-helix, beta-sheet, and other structures, which are crucial elements in the comparison of the protein structures. Quantitation of infrared spectra of papain-solubilized HLA-A2, HLA-B7, and DR1 in phosphate buffer gave alpha-helix contents of 17%, 8%, and 10% and beta-sheet contents of 41%, 48%, and 53%, respectively. By circular dichroism, papain-solubilized HLA-A2, HLA-B7, and DR1 were also found to have comparable alpha-helix contents (e.g., 8%, 20%, and 17%, respectively). Circular dichroism analysis for beta-sheet gave 29% for papain-solubilized HLA-B7 and 42% for papain-solubilized DR1. The value for papain-solubilized HLA-A2 (74%) was anomalous. It is proposed that Trp-107 of HLA-A2, missing in both HLA-B7 and DR1, may be responsible for much of the anomaly. Due to the uncertainties inherent in quantitation of the amounts of secondary structures by both spectral methods, the differences in the contents of alpha-helix and beta-sheet in the three proteins are not considered significant. However, differences in the nature of the beta-sheet structures are suggested by infrared spectroscopy. These results provide physical evidence for an overall structure of class II antigens modeled on that of class I antigens.
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Affiliation(s)
- J C Gorga
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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89
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Shimada H, Dong A, Matsushima-Hibiya Y, Ishimura Y, Caughey WS. Distal His----Arg mutation in bovine myoglobin results in a ligand binding site similar to the abnormal beta site of hemoglobin Zurich (beta 63 His----Arg). Biochem Biophys Res Commun 1989; 158:110-4. [PMID: 2912443 DOI: 10.1016/s0006-291x(89)80184-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Carbon monoxide binding to a myoglobin mutant with distal arginine in place of histidine has been examined. The mutant is derived from a cDNA clone for Mb mRNA from fetal bovine skeletal muscle. The mutation only slightly perturbs visible/Soret spectra whereas the infrared spectrum of liganded CO is greatly modified to become nearly identical to Hb Zurich beta-subunit spectrum. The mutant IR spectra differ substantially from spectra of wild-type MbCO and normal HbCO beta-subunit. For both the Mb and the Hb the distal His----Arg mutation increases the affinity for CO and reduces the number of observed conformers. These results demonstrate that this mutation greatly reduces the differences between Mb and Hb in the structure and properties of its ligand binding sites.
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Affiliation(s)
- H Shimada
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
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90
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Abstract
Methods for obtaining the infrared spectrum of a single erythrocyte by infrared microscopy have been developed. The spectrum contains the amide I, II, and III bands characteristic of protein secondary structure near 1650, 1550, and 1300 cm-1, respectively. Bound carbon monoxide exhibits a readily measured band at 1951 cm-1 for 12C16O and 1907 cm-1 for 13C16O. Both amide and CO bands are similar to those found for purified hemoglobin A. Spectra can be obtained in H2O or D2O media under physiologically relevant conditions. Single cell infrared spectroscopy (SCIR) permits the qualitative and quantitative determination of differences among individual red cells. These results suggest many potential applications for SCIR for the measurements of properties of individual cells at the molecular level under physiologically relevant conditions.
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Affiliation(s)
- A Dong
- Department of Biochemistry, Colorado State University, Fort Collins 80523
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91
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Sowa S, Dong A, Roos EE, Caughey WS. The anesthetic nitrous oxide affects dioxygen utilization by bovine heart and bean seed mitochondrial particles. Biochem Biophys Res Commun 1987; 144:643-8. [PMID: 3034260 DOI: 10.1016/s0006-291x(87)80014-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nitrous oxide affects dioxygen utilization by both bean seed and bovine heart submitochondrial particles when either succinate or reduced cytochrome c are used as substrates. Bovine heart particles exhibit reversible, dose-dependent partial inhibition of respiratory activity when exposed to N2O. Bean seed particle respiration is stimulated by low levels of N2O, but higher concentrations are inhibitory. These findings can be explained in terms of one locus of anesthetic action: cytochrome c oxidase, the terminal component of the mitochondrial respiratory chain. Alterations in respiration rates are expected to make important contributions to anesthesia in animals and to control of germination in plants.
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92
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Dong A. Health care employees with AIDS--set policies before problems arise. Dimens Health Serv 1986; 63:43. [PMID: 3758528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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93
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Chou CK, Guy AW, McDougall JA, Dong A, Luk KH. Thermographically determined specific absorption rate patterns of 434-MHz applicators. Med Phys 1986; 13:385-90. [PMID: 3724699 DOI: 10.1118/1.595880] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The specific absorption rate (SAR) patterns of two 434-MHz hyperthermia applicators, models TCA 434-1 (9 X 20 cm) and TCA 434-2 (13 X 25 cm), were evaluated thermographically using a phantom model. The phantom model consisted of a 2-cm-thick layer of fat and a 10-cm depth of muscle contained in a 30 X 30 cm base Plexiglas box. The model was bisected in the middle. Polyester screens at the interface allowed the synthetic gel to make electrical contact between the two halves of the muscle tissue. Octyl alcohol was applied to the fat interface to ensure continuity of dielectric properties. Thermograms were taken for both applicators over the following areas of the exposed model: (1) fat surface, (2) internal surface with E-field parallel to interface, and (3) internal surface with E-field perpendicular to interface. SAR's were calculated from the temperature rise (8 degrees C maximum), net input power (550-650 W), exposure time (15-60 s), and specific heat of the muscle (0.86 kcal/kg degrees C). A factor of 0.42 needs to be multiplied to correct for the specific heat of fat. High localized SAR's along the broad sides of the applicators were seen when the applicators were in direct contact with the phantom. With the use of a 0.8-cm polystyrene foam spacing, the SAR's within the aperture of the applicators were relatively uniform. The patterns of the two applicators were quite similar. However, the TCA 434-1 applicator is smaller and more applicable for clinical conditions.
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94
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Tuffnell PG, Gannon MT, Dong A, DeBoer G, Erlichman C. Limitations of urinary mutagen assays for monitoring occupational exposure to antineoplastic drugs. Am J Hosp Pharm 1986; 43:344-8. [PMID: 3513557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The sensitivity of the Salmonella reversion test of Ames as a screen for accidental absorption of 17 antineoplastic agents by drug handlers was evaluated. Dilutions of each drug were added to agar inoculated with each of two Salmonella typhimurium strains (TA98 and TA100); control plates contained no test drug. Colonies were counted after incubation at 36 degrees C for 48 hours. The drugs were tested in the presence of a liver preparation to provide metabolic activation of mutagenicity. Urine samples collected from patients after doses of three mutagenic drugs were extracted and tested with the Ames test. For 11 of the 17 drug solutions, no mutagenic activity was seen, but many of these 11 were toxic to the organisms. The most highly mutagenic drugs were doxorubicin and cisplatin, with mechlorethamine, carmustine, dacarbazine, and cyclophosphamide exhibiting less mutagenic activity. Urine from patients treated with doxorubicin or cyclophosphamide showed mutagenicity, but the results suggested that the quantity of these drugs that would have to be absorbed to produce a definite reaction in urine is unlikely to be achieved by drug handlers who use standard precautions. Because of its lack of sensitivity and the potential effects of environmental and dietary factors on the results, this bacterial mutagenicity test should not be used routinely for detection of accidental absorption of antineoplastic drugs.
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95
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Abstract
Serum vitamin B12 and complete blood count values were determined for 83 volunteer subjects from an American vegetarian society conference (USA). Among subjects who did not supplement their diets with vitamin B12 or multiple vitamin tablets, 92% of the vegans (total vegetarians), 64% of the lactovegetarians, 47% of the lacto-ovovegetarians and 20% of the semivegetarians had serum vitamin B12 levels less than 200 pg/ml (normal = 200-900 pg/ml). However, their complete blood count values did not deviate greatly from those found for nonvegetarians, even though some had been vegans or lactovegetarians for over 10 years. Macrocytosis among the vegetarians was minimal; none had mean corpuscular volume greater than 103 fl.
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96
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Leers WD, Kouroupis GM, Dong A. Feasibility of routine testing for hepatitis B surface antigen in hospital employees and restriction of carriers. Can Med Assoc J 1976; 115:995-8. [PMID: 1032590 PMCID: PMC1878876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In 1972-73, 48 hospital staff members were tested selectively for hepatitis B surface antigen (HBsAg); 4 (8.3%) were found to be HBsAg-positive. In 1974-75, 1415 staff members were tested routinely before employment and at periodic health examination; 25 (1.8%) were found to be HBsAg-positive. Of the HBsAg-positive staff members 55.2% were Asians, this proportion being significantly (P less than 0.05) greater than that of any other ethnic group, and 31.0% were southern Europeans. Nurses and laboratory technologists were the largest professional groups among the HBsAg-positive staff, each accounting for 20.7%. Our results indicate that it is impractical to carry out routine testing of hospital staff for HBsAg. Selective testing and restriction from work in their units is proposed for staff of the renal and peritoneal dialysis units, the emergency department and the intravenous team and dietary staff who handle food directly.
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97
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98
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Abstract
When 75Se, as selenite, is added to human blood it is rapidly taken up by the cells (50–70% within 1–2 min) and is then released into the plasma so that most of the radioactivity is in the plasma by 15–20 min. Uptake is inhibited by 10−3 M cyanide. The release of radioactivity from the cells is inhibited by 10−3 M para-chloromercuribenzoate and by 10−3 M iodoacetamide, although these agents do not affect uptake. Azide and 2,4-dinitrophenol (at 10−3 M) do not affect either process. Large quantities of sulfite, sulfate, and selenate (1000 times as much S or Se as 75Se) do not affect uptake or release, but large amounts of selenite (1000 times) inhibit release. The release rate follows first-order kinetics and increases with temperature. 75Se released from cells is bound by a plasma protein but can be removed from the protein by treatment with cysteine. Studies suggest that the released selenium is in an altered form or state, although this product has not been characterized. A hypothetical pathway for the metabolism of selenium is presented to account for the observations.
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