| 1. |
- Kim, S.K., et al.
(författare)
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Binding Geometries of Triple Helix Selective Benzopyrido [4,3-b]indole Ligands Complexed with Double- and Triple-Helical Polynucleotides
- 1997
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Ingår i: Biopolymers. - 0006-3525 .- 1097-0282. ; 42:1, s. 101-111
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Tidskriftsartikel (refereegranskat)abstract
- The binding modes of three benzopyrido[4,3-b]indole derivatives (and one benzo[f]pyrido[4-3b]quinoxaline derivative) with respect to double helical poly(dA) . poly(dT) and poly[d(A-T)](2) and triple-helical poly(dA) . 2poly(dT) have been investigated using linear dichroism (LD) and CD: (I) 3-methoxy-11-amino-BePI where BePI = {7H-8-methyl-benzo[e]pyrido[4,3-b]indole}, (II) 3-methoxy-11-[(3'-amino)propylamino]-BePI, (III) 3-methoxy-7-[(3'diethylamino)propylamino]BgPI where BgPI = {benzo[g]pyrido[4,3-b]indole}, and (IV) 3-methoxy-11-[(3'amino)propylamino]BfPQ where BfPQ = {benzo[f]pyrido[4-3b]quinoxaline}. The magnitudes of the reduced LD of the electronic transitions of the polynucleotide bases and of the bound ligands are generally very similar, suggesting an orientation of the plane of the ligands' fused-ring systems preferentially perpendicular to the helix axis. The LD results suggest that all of the ligands are intercalated for all three polynucleotides. The induced CD spectrum of the BePI chromophore in the (II-BePI)-poly[d(A-T)](2) complex is almost a mirror image of that for the (I-BePI)-poly(dA) . poly(dT) and (I-BePI)-poly(dA) . 2poly(dT) complexes, suggesting an antisymmetric orientation of the BePI moiety upon intercalation in poly[d(A-T)]2 compared to the other polynucleotides. The induced CD of I-BePI bound to poly(dA) . 2poly(dT) suggests a geometry that is intermediate between that of its other two complexes. The concluded intercalative binding as well as the conformational variations between the different BePI complexes are of interest in relation to the fact that BePI derivatives are triplex stabilizers.
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| 2. |
- Behravan, G., et al.
(författare)
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THE INTERACTION OF ELLIPTICINE DERIVATIVES WITH NUCLEIC-ACIDS STUDIED BY OPTICAL AND H-1-NMR SPECTROSCOPY - EFFECT OF SIZE OF THE HETEROCYCLIC RING
- 1994
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 34:5, s. 599-609
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Tidskriftsartikel (refereegranskat)abstract
- The DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly [(dA-dT).(dA-dT)], or poly [(dG-dC).(dG-dC)] showed a 10 nm bathochromic shift of the light absorption bands of the pentacyclic and tetracyclic compounds upon binding to the nucleic acids, which indicates binding by intercalation. For the tricyclic compound a smaller shift of 1-3 nm was observed upon binding to the nucleic acids. Flow linear dichroism studies show that the geometry of all complexes is consistent with intercalation of the ring system, except for the DNA and poly [(dG-dC).(dG-dC)] complexes of the tricyclic compound, where the average angle between the drug molecular plane and the DNA helix axis was found to be 65 degrees. One-dimensional H-1-nmr spectroscopy was used to study complexes between d(CGCGATCGCG)(2) and the tricyclic and pentacyclic compounds. The results on the pentacyclic compound show nonselective broadening due to intermediate chemical exchange of most oligonucleotide resonances upon drug binding. The imino proton resonances are in slow chemical exchange, and new resonances with upheld shifts approaching 1 ppm appear upon drug binding, which supports intercalative binding of the pentacyclic compound. The results on the tricyclic compound show more rapid binding kinetics and very selective broadening of resonances. The data suggest that the tricyclic compound is in an equilibrium between intercalation and minor groove binding, with a preference to bind close to the AT base pairs with the side chain residing in the minor groove. (C) 1994 John Wiley and Sons, Inc.
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| 3. |
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| 4. |
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| 5. |
- Blanch, Ewan W, et al.
(författare)
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Raman optical activity characterization of native and molten globule states of equine lysozyme : comparison with hen lysozyme and bovine alpha-lactalbumin
- 2000
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Ingår i: Biopolymers. - 0006-3525 .- 1097-0282. ; 57:4, s. 235-248
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Tidskriftsartikel (refereegranskat)abstract
- Vibrational Raman optical activity (ROA) spectra of the calcium-binding lysozyme from equine milk in native and nonnative states are measured and compared with those of the homologous proteins hen egg white lysozyme and bovine alpha-lactalbumin. The ROA spectrum of holo equine lysozyme at pH 4.6 and 22 degrees C closely resembles that of hen lysozyme in regions sensitive to backbone and side chain conformations, indicating similarity of the overall secondary and tertiary structures. However, the intensity of a strong positive ROA band at approximately 1340 cm(-1), which is assigned to a hydrated form of alpha helix, is more similar to that in the ROA spectrum of bovine alpha-lactalbumin than hen lysozyme and may be associated with the greater flexibility and calcium-binding ability of equine lysozyme and bovine alpha-lactalbumin compared with hen lysozyme. In place of a strong sharp positive ROA band at approximately 1300 cm(-1) in hen lysozyme that is assigned to an alpha helix in a more hydrophobic environment, equine lysozyme shows a broader band centered at approximately 1305 cm(-1), which may reflect greater heterogeneity in some alpha-helical sequences. The ROA spectrum of apo equine lysozyme at pH 4.6 and 22 degrees C is almost identical to that of the holo protein, which indicates that loss of calcium has little influence on the backbone and side chain conformations, including the calcium-binding loop. From the similarity of their ROA spectra, the A state at pH 1.9 and both 2 and 22 degrees C and the apo form at pH 4.5 and 48 degrees C, which are partially folded denatured (molten globule or state A) forms of equine lysozyme, have similar structures that the ROA suggests contain much hydrated alpha helix. The A state of equine lysozyme is shown by these results to be more highly ordered than that of bovine alpha-lactalbumin, the ROA spectrum of which has more features characteristic of disordered states. A positive tryptophan ROA band at approximately 1551 cm(-1) in the native holo protein disappears in the A state, which is probably due to the presence of nonnative conformations of the tryptophans associated with a previously identified cluster of hydrophobic residues.
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| 6. |
- Burman, Robert, 1979-, et al.
(författare)
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Evaluation of toxicity and anti-tumour activity of cycloviolacin O2 in mice.
- 2010
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 94:5, s. 626-634
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Tidskriftsartikel (refereegranskat)abstract
- Cycloviolacin O2 is a small cyclic cysteine-rich protein belonging to the group of plant proteins called cyclotides. This cyclotide has been previously shown to exert cytotoxic activity against a variety of human tumor cell lines as well as primary cultures of human tumor cells in vitro. This study is the first evaluation of its tolerability and antitumor activity in vivo. Maximal-tolerated doses were estimated to 1.5 mg/kg for single intravenous (i.v.) dosing and 0.5 mg/kg for daily repeated dosing, respectively. Two different in vivo methods were used: the hollow fiber method with single dosing (i.v. 1.0 mg/kg) and traditional xenografts with repeated dosing over 2 weeks (i.v. 0.5 mg/kg daily, 5 days a week). The human tumor cell lines used displayed dose-dependent in vitro sensitivity (including growth in hollow fibers to confirm passage of cycloviolacin O2 through the polyvinylidene fluoride fibers), with IC50 values in the micromolar range. Despite this sensitivity in vitro, no significant antitumor effects were detected in vivo, neither with single dosing in the hollow fiber method nor with repeated dosing in xenografts. In summary, the results indicate that antitumor effects are minor or absent at tolerable (sublethal) doses, and cycloviolacin O2 has a very abrupt in vivo toxicity profile, with lethality after single injection at 2 mg/kg, but no signs of discomfort to the animals at 1.5 mg/kg. Repeated dosing of 1 mg/kg gave a local-inflammatory reaction at the site of injection after 2–3 days; lower doses were without complications.
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| 7. |
- Bäcklund, Fredrik G., et al.
(författare)
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Controlling Amyloid Fibril Formation by Partial Stirring
- 2016
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Ingår i: Biopolymers. - : Wiley-Blackwell. - 0006-3525 .- 1097-0282. ; 105:5, s. 249-259
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Tidskriftsartikel (refereegranskat)abstract
- Many proteins undergoes self-assembly into fibrillar structures known as amyloid fibrils. During the self-assembly process related structures, known as spherulites, can be formed. Herein we report a facile method where the balance between amyloid fibrils and spherulites can be controlled by stirring of the reaction mixture during the initial stages of the self-assembly process. Moreover, we report how this methodology can be used to prepare non-covalently functionalized amyloid fibrils. By stirring the reaction mixture continuously or for a limited time during the lag phase the fibril length, and hence the propensity to form liquid crystalline phases, can be influenced. This phenomena is utilized by preparing films consisting of aligned protein fibrils incorporating the laser dye Nile red. The resulting films display polarized Nile red fluorescence.
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| 8. |
- Carlsson, C., et al.
(författare)
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Experimental and simulated fluorescence depolarization due to energy transfer as tools to study DNA-dye interactions
- 1997
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Ingår i: Biopolymers. - 0006-3525 .- 1097-0282. ; 41:5, s. 481-494
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Tidskriftsartikel (refereegranskat)abstract
- A method to study DNA-dye complexes by the combination of steady state fluorescence anisotropy measurements and computer simulations of the fluorescence depolarization due to resonance energy transfer is presented. The simulations are based on a Markov chain analysis, assuming random distribution of the dyes along the DNA chain and energy transfer that obeys Forster kinetics. Since the investigated intercalators (ethidium bromide, YO, PO) and groove binders [4'6-diamidino-2-phenylindole (DAPI)] were found to show different depolarization dependence on binding density, the method can be used to quite sensitively characterize the binding mode. Excellent agreement between the measured and simulated anisotropy is found for all investigated intercalators. The proposed method gives an estimation of the unwinding angle for intercalators and provides information about the binding site size, and the presence or absence of sequence specificity. For the groove binder DAPI interacting with mixed sequenced DNA, the measured and computed depolarization do not agree, and this can be rationalized in terms of the high sequence specificity of this dye. However, for DAPI bound to [poly(dA-dT)](2) the measured data agree well with computed data for a groove binder that is displaced a distance 7 Angstrom from the helix axis and has a binding site size of three bases. (C) 1997 John Wiley & Sons, Inc.
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| 9. |
- Craik, David J., et al.
(författare)
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Nomenclature of homodetic cyclic peptides produced from ribosomal precursors : An IUPAC task group interim report
- 2016
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 106:6, s. 917-924
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Tidskriftsartikel (refereegranskat)abstract
- In 2015, an International Union of Pure and Applied Chemistry (IUPAC) Task Group was formed to develop nomenclature recommendations for homodetic cyclic peptides produced from ribosomal precursors. Delegates of the 2015 International Conference on Circular Proteins (ICCP) were presented with the strengths and weaknesses of four published approaches to homodetic cyclic peptide nomenclature, and a summary of the ensuing discussion is presented here. This interim report presents a potentially novel suggestion-the use of Cahn-Ingold-Prelog rules to specify amino acid priority in homodetic peptides for consistent numbering. Indeed, this might be the first extension of the Cahn-Ingold-Prelog rules in five decades. The authors invite interested parties to contact the corresponding author with suggestions for the improvement of the proposed nomenclature; these ideas will be discussed and considered for inclusion in the final report.
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| 10. |
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| 11. |
- Doglia, S. M., et al.
(författare)
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QUINACRINE - SPECTROSCOPIC PROPERTIES AND INTERACTIONS WITH POLYNUCLEOTIDES
- 1993
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 33:9, s. 1431-1442
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Tidskriftsartikel (refereegranskat)abstract
- The acridine dye quinacrine and its interactions with calf thymus DNA, poly(dA-dT).poly(dA-dT), and poly(dG-dC).poly(dG-dC) were studied by light absorption, linear dichroism, and fluorescence spectroscopy. The transition moments of quinacrine give rise to absorption bands polarized along the short axis (400-480-nm band), and the long axis (345-nm and 290-nm bands) of the molecule, respectively. Linear dichroism studies show that quinacrine intercalates into calf thymus DNA as well as into the polynucleotides, displaying fairly homogeneous binding to poly (dA-dT).poly(dA-dT), but more than one type of intercalation site for calf thymus DNA and poly(dG-dC).poly(dG-dC). Fluorescence spectroscopy shows that for free quinacrine the pK = 8.1 between the mono- and diprotonated states also remains unchanged in the excited state. Quinacrine bound to calf thymus DNA and polynucleotides exhibits light absorption typical for the intercalated diprotonated form. The fluorescence enhancement of quinacrine bound to poly (dA-dT).poly(dA-dT) may be due to shielding from water interactions involving transient H-bond formation. The fluorescence quenching in poly (dG-dC).poly (dG-dC) may be due to excited state electron transfer from guanine to quinacrine. (C) 1993 John Wiley & Sons, Inc.
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| 12. |
- Ekblad, Torun, et al.
(författare)
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Synthesis and chemoselective intramolecular cross-linking of a HER2-binding Affibody
- 2009
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 92:2, s. 116-123
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Tidskriftsartikel (refereegranskat)abstract
- The human epidermal growth factor receptor HER2 has emerged as an important target for molecular imaging of breast cancer. This article presents the design and synthesis of a HER2-targeting affibody molecule with improved stability and tumor targeting capacity, and with potential use as an imaging agent. The 58 aa three-helix bundle protein was assembled using solid-phase peptide synthesis, and a chemoselective ligation strategy was used to establish an intramolecular thioether bond between the side chain thiol group of a cysteine residue, positioned in the loop between helices I and II, and a chloroacetyl group on the side chain amino group of the C-terminal lysine residue. The tethered protein offered an increased thermal stability, with a melting temperature of 64 degrees C, compared to 54 degrees C for the linear control. The ligation did not have a major influence on the HER2 binding affinity, which was 320 and 380 pM for the crosslinked and linear molecules, respectively. Biodistribution studies were performed both in normal and tumor-bearing mice to evaluate the impact of the crosslinking on the in vivo behavior and on the tumor targeting performance. The distribution pattern was characterized by a low uptake in all organs except kidney, and rapid clearance from blood and normal tissue. Crosslinking of the protein resulted in a significantly increased tumor accumulation, rendering the tethered HER2-binding affibody molecule a valuable lead in the development of superior HER2 imaging agents.
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| 13. |
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| 14. |
- Galanakis, Petros A., et al.
(författare)
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Study of the Interaction Between the Amyloid Beta Peptide (1-40) and Antioxidant Compounds by Nuclear Magnetic Resonance Spectroscopy
- 2011
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 96:3, s. 316-327
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Tidskriftsartikel (refereegranskat)abstract
- Amyloid beta peptide (Aβ) aggregation leads to the senile plaque formation, a process that is strongly influenced by oxidative stress and is considered as the molecular basis of various neurodegenerative diseases, such as Alzheimer's Disease (AD). Endogenous antioxidants or dietary derived compounds may down-regulate this process. In this study, the interaction of two antioxidants, oleuropein (OE) and melatonin (M) with Aβ, is monitored through NMR spectroscopy and Mass Spectrometry. The concerted application of these two analytical techniques provides new experimental evidence and residue-specific insights into the interacting Aβ peptide amino acids that are implicated in this process. Both antioxidant compounds interact in a similar way with the peptide and cause chemical shift variations. The most pronounced resonance changes have been observed for the (1)H-(15)N signals of N-terminal region and Leu(17)-Phe(20) residues, as monitored by NMR titration studies.
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| 15. |
- Galanis, Athanassios S, et al.
(författare)
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Enhanced microwave-assisted method for on-bead disulfide bond formation: synthesis of alpha-conotoxin MII.
- 2009
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 92:1, s. 23-34
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Tidskriftsartikel (refereegranskat)abstract
- A novel enhanced microwave-assisted disulfide bridge formation method has been developed. To optimize the synthesis of the biologically important bicyclic peptide alpha-conotoxin MII (alpha-CtxMII), several cyclization methods have been tested and are discussed herein. By using m.w.-assisted heating, we achieved high yields for the first loop cyclization of alpha-CtxMII on-bead. This method has the advantage of avoiding intermolecular by-products during the cyclization step. Furthermore, the method gives higher yields compared with the common on-bead cyclization methods. The second disulfide bridge of alpha-CtxMII was formed using a simple oxidation method after the cleavage of the intermediate monocyclic peptide from the resin. This method has the potential to be efficient for the synthesis of other disulfide rich biologically important peptides.
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| 16. |
- Gerlach, Samantha L., et al.
(författare)
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A Systematic Approach to Document Cyclotide Distribution in Plant Species from Genomic, Transcriptomic, and Peptidomic Analysis
- 2013
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 100:5, s. 433-437
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Tidskriftsartikel (refereegranskat)abstract
- Cyclotides are a large family of plant peptides characterized by their cyclic cystine knot composed of a circular backbone and three disulfide bonds that impart exceptional stability. They, and several acyclic variants, have been isolated from plants within the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, Solanaceae, and Poaceae families. A variety of chemical and genetic approaches have been applied for the discovery and characterization of cyclotides. As investigations of cyclotide expression, distribution, and phylogeny rapidly increase, the authors have proposed the inclusion of information pertaining to plant species that have been analyzed but do not appear to express cyclotides into the CyBase database. CyBase is dedicated to providing web tools and information about cyclic peptides and proteins to the scientific community. Including detailed information about sampling and analysis parameters of plant species that have been investigated but not published elsewhere should assist in the process of selecting species for establishing new cyclotide discovery projects, as well as for detailed reanalysis using alternative technical approaches. In summary, the collection and deposition of all plant species that have been examined (whether cyclotides have been found or not) would help to impart a deeper understanding of cyclotide discovery, evolution, and physiological function.
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| 17. |
- Gerlach, Samantha L., et al.
(författare)
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Anticancer and Chemosensitizing Abilities of Cycloviolacin O2 from Viola odorata and Psyle Cyclotides from Psychotria leptothyrsa
- 2010
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 94:5, s. 617-625
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Tidskriftsartikel (refereegranskat)abstract
- Cycloviolacin O2 (CyO2), a cyclotide from Viola odorata (Violaceae) has antitumor effects and causes cell death by membrane permeabilization. In the breast cancer line, MCF-7 and its drug resistant subline MCF-7/ADR, the cytotoxic effects of CyO2 (0.2-10 mu M) were monitored in the presence and absence of doxorubicin (0.1-5 mu M) using cell proliferation assays to establish its chemosensitizing abilities. SYTOX Green assays were performed to verify membrane permeabilization and showed cellular disruption correlates with cyclo tide chemosensitization. Fluorescence microscopy studies demonstrated increased cellular internalization of doxorubicin in drug resistant cells when coexposed to CyO2. Interestingly, CyO2 did not produce significant membrane disruption in primary human brain endothelial cells, which suggested cyclo tide specificity toward induced pore formation in highly proliferating tumor cells. Furthermore, three novel cyclotides (psyle A, C and E) from Psychotria leptothyrsa (Rubiaceae) were also monitored for cytotoxic activity. The cyclotides displayed potent cytotoxicity (IC50 = 0.64->10 mu M), and coexposure to cyclotides significantly enhanced doxorubicin induced toxicity (IC50 = 0.39-0.76 mu M). This study documents several cyclotides with robust cytotoxicity that may be promising chemosensitizing agents against drug resistant breast cancer.
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| 18. |
- Gerlach, Samantha L., et al.
(författare)
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Cycloviolacin O2 (CyO2) Suppresses Productive Infection and Augments the Antiviral Efficacy of Nelfinavir in HIV-1 Infected Monocytic Cells
- 2013
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 100:5, s. 471-479
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Tidskriftsartikel (refereegranskat)abstract
- Human immunodeficiency virus type-1 (HIV-1), the etiologic agent of acquired immune deficiency syndrome (AIDS), is a global pandemic causing millions of deaths annually. Highly active antiretroviral therapy (HAART) greatly enhances lifespan but eventually causes debilitating side effects, in part, due to their chronic administration required to suppress HIV-1 replication. If treatment is discontinued, viral suppression is lost and dormant replication-competent monocytic cell reservoirs become reactivated, leading to viral recrudescence and progression to AIDS. Therefore, novel strategies to circumvent obstacles to HIV-1 therapy are critically needed. We evaluated the potentially therapeutic effects of cycloviolacin O2 (CyO2) on cell viability (MTTassay), membrane disruption (SYTOX Green uptake), p24 production [enzyme-linked immunosorbent assays (ELISA)], and proviral integration (PCR amplification) in U1 cells; a monocytic cell model of HIV-1 latency and reactivation. We demonstrate, for the first time, that CyO2 (0.5-5.0 mu M) kills productively infected cells. Sub-toxic concentrations (< 0.5 mu M) of CyO2 disrupted plasma membranes in both latently-infected and productively-infected U1 cells and enhanced the antiviral efficacy of nelfinavir, a HIV-1 protease inhibitor (HPI). Interestingly, CyO2 also decreased virus production by activated U1 cells; however, this effect was not due to suppression of integrated provirus in U1 cells. This suggested that, in addition to the known pore-forming ability of cyclotides, a novel mode of antiviral activity may exist for CyO2. Our data indicate that CyO2 may be a promising candidate for the targeting HIV-1 reservoirs in monocytes, and their inclusion in adjuvant therapy approaches may augment the efficacy of HPIs and ultimately facilitate virus elimination.
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| 19. |
- Gonzalez Rodriguez, Adrian, 1988, et al.
(författare)
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Melting transition of oriented Li-DNA fibers submerged in ethanol solutions
- 2021
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 112:3
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Tidskriftsartikel (refereegranskat)abstract
- The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water. They become weaker still and the DNA less stable as the ethanol concentration increases but, conversely, the fibers become more compact and the distances between base pairs become more regular. The results show that the melting transition is relatively insensitive to local confinement and depends more on the interaction between the DNA and its aqueous environment.
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| 20. |
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| 21. |
- Hederos (Håkansson), Sofia, et al.
(författare)
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Nucleophile Selectivity in the Acyl Transfer Reaction of a Designed Enzyme
- 2005
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Ingår i: Biopolymers. - : John Wiley & Sons. - 0006-3525 .- 1097-0282. ; 79:6, s. 292-299
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Tidskriftsartikel (refereegranskat)abstract
- The acyl transfer reaction of S-glutathionyl benzoate (GSB) is catalyzed by a rationally designed mutant of human glutathione transferase A1-1, A216H. The catalyzed reaction proceeds via the formation of an acyl intermediate and has been studied in the presence of nitrogen, oxygen, and sulfur nucleophiles to determine the selectivity with regards to nucleophile structure. Methanol was previously shown to react with the acyl intermediate and form the corresponding ester, methylbenzoate, under a significant rate enhancement. In the present investigation, the dependence on nucleophile structure and reactivity has been investigated. Ethane thiol gave rise to a larger rate enhancement in the enzyme-catalyzed reaction than ethanol, whereas ethylamine did not increase the reaction rate. The reactivities toward the acyl intermediate of primary and secondary alcohols with similar pKa values depended on the structure of the aliphatic chain, and 1-propanol was the most efficient alcohol. The reactivity of the oxygen nucleophiles was also found to depend strongly on pKa as 2,2,2-trifluoroethanol, with a pKa of 12.4, was the most efficient nucleophile of all that were tested. Saturation kinetics was observed in the case of 1-propanol, indicating a second binding site in the active site of A216H. The nucleophile selectivity of A216H provides the knowledge base needed for the further reengineering of A216H towards alternative substrate specificities.
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| 22. |
- Holm, Anne I. S., et al.
(författare)
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Synchrotron Radiation Circular Dichroism of Various G-Guadruplex Structures
- 2010
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 93:5, s. 429-433
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Tidskriftsartikel (refereegranskat)abstract
- Here we report synchrotron radiation circular dichroism spectra of various G-quadruplexes from 179 to 350 nm, and a number of bands in the vacuum ultraviolet (VUV) are reported for the first time. For a tetramolecular parallel structure, the strongest band in the spectrum is a negative band in the VUV at 182 nm; for a bimolecular antiparallel structure with diagonal loops, a new strong positive band is found at 190 nm; for a bimolecular parallel structure with edgewise loops, a strong positive band at 189 nm is observed; and for a self-folded chair-type structure, the strongest band in the spectrum is a positive band at 187 nm. For the tetramolecular parallel structure, the CD signals at all wavelengths are dominated by contributions from quartets of G bases, and the signal strength is approximately proportional to the number of quartets. Our experiments on well-characterized G-quadruplex structures lead us to question past attributions of CD signals to helix handedness and G quartet polarity. Although differences can be observed in the VUV region for the various quadruplex types, there do not appear to be clear-cut spectral features that can be used to identify specific topological features. It is suggested that this is because a dominant positive band in the VUV seen near 190 nm in all quadruplex structures is due to intrastrand guanine guanine base stacking. However, our spectra can serve as reference spectra for the G-quadruplex structures investigated and, not least, to benchmark theoretical calculations and empirical models.
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| 23. |
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| 24. |
- Jonsson, Mats, 1939, et al.
(författare)
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Orientation of DNA during gel electrophoresis studied with linear dichroism spectroscopy
- 1988
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Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 27:3, s. 381-414
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Tidskriftsartikel (refereegranskat)abstract
- A method for in situ study of orientation of DNA during gel electrophoresis has been developed. Linear dichroism spectra measured by this phase-modulation technique can sensitively and selectively detect orientation of DNA during electrophoretic migration in gel. [Measurement of “electrophoretic orientation” was first reported in 1985 by B. Åkerman, M. Jonsson, and B. Nordén (1985) (J. Chem. Soc. Chem. Commun. 422–423)]. Restriction fragments of duplex DNA of lengths in the ranges of 300–2319 base pairs (bp) and 4361–23130 bp have been studied in 5% polyacrylamide and 1% agarose gels, respectively. The fragments become preferentially oriented with the DNA helix axis parallel to the migration direction. In agarose the orientation is found to increase sigmoidally, and in polyacrylamide, linearly, with the electric field strength, within the field ranges accessible to measurement (0–40 and 5–40 V/cm, respectively). In both types of gels a considerable increase in orientation with length of DNA was observed. Compared to dipole orientation in electric fields, the electrophoretic orientation is high: orientation factor S = 0.027 in agarose for 23130 bp at 10 V/cm and S = 0.004 in polyacrylamide for 2319 bp at 10 V/cm. In addition to orientation of DNA, the electrophoresis also leads to orientation effects in the gel structure owing to Joule heating. In agarose there is also an effect that is associated with the migrating DNA zones and that produces different orientations of the gel at the front and rear parts of a zone. Evidence is presented that this effect is due to a DNA-induced electroosmotic flow causing a contraction of the gel in the front of the zone and an expansion in the rear. The experimental results on DNA orientation are compared with the reptation theories for gel electrophoresis. The theory of Lumpkin et al. [O. J. Lumpkin, P. Dejardin, and B. H. Zimm (1985) Biopolymers24, 1573–1593] predicts no orientation length dependence, but it does predict a shape of the field dependence that resembles the shape observed in agarose. The theory of Slater and Noolandi [G. W. Slater and J. Noolandi (1986) Biopolymers25, 431–454] predicts an orientational length dependence that is an order of magnitude less than the experimental one, and a field dependence that agrees neither with the sigmoidal shape observed in agarose nor with the linear dependence in polyacrylamide.
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| 25. |
- Joseph, P., et al.
(författare)
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Morphology of lignin structures on fiber surfaces after organosolv pretreatment
- 2022
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Ingår i: Biopolymers. - : John Wiley and Sons Inc. - 0006-3525 .- 1097-0282. ; 113:9
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Tidskriftsartikel (refereegranskat)abstract
- The redeposition of lignin to the fiber surface after organosolv pretreatment was studied using two different reactor types. Results from the conventional autoclave reactor suggest that redeposition occurs during the cooling down stage. Redeposited particles appeared to be spherical in shape. The size and population density of the particles depends on the concentration of organosolv lignin in the cooking liquor, which is consistent with the hypothesis that reprecipitation of lignin occurs when the system is cooled down. The use of a displacement reactor showed that displacing the spent cooking liquor with fresh cooking liquor helps in reducing the redeposition and the inclusion of a washing stage with fresh cooking liquor reduced the reprecipitation of lignin, particularly on the outer fiber surfaces. Redeposition of lignin was still observed on regions that were less accessible to washing liquid, such as fiber lumens, suggesting that complete prevention of redeposition was not achieved. © 2022 The Authors.
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