摘要:

AbstractUsing classical potential functions, we carried out potential‐energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum‐energy conformations of the complexes are close to DNA A‐ and B‐family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low‐energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200102

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractTo exemplify the usefulness of theS‐tert‐butylthio group for a reversible blocking of the cysteine thiol function in peptide synthesis, fully protected dihydrosomatostatin was prepared by the fragment‐condensation procedure. The experimental results confirm the excellent stability of the asymmetric disulfide under the normal conditions of peptide synthesis and prove that the selective, acid‐catalyzed nucleophil removal—as well as by mercaptans—of the 2‐nitrophenylsulfenyl group proceeds smoothly in the presence of this thiol protection. Thus, the strategy of overall acid‐labile side‐chain protection in combination with theNα‐2‐nitrophenylsulfenyl group for the chain‐elongation steps can be successfully applied to the synthesis of cysteine‐containing peptides using theirS‐tert‐butylthio derivatives. Removal of the acid‐labile groups, followed by reductive cleavage of the asymmetric disulfides and successive air oxidation, allowed a clean conversion of protected dihydrosomatostatin into somatostatin at a high deg

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200103

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractWe studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod‐Wyman‐Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this con

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200104

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractWe studied the effects of methanol, ethanol,iso‐propanol, andn‐propanol on the reaction of hemoglobin with oxygen at various temperatures. The analysis of the results in terms of the Monod‐Wyman‐Changeux model allowed determination of the overall contribution of the alcohols to the standard enthalpy and entropy differences between the T and R states of hemoglobin. A phenomenological approach allowed us to obtain separately the contributions related to the variations of the bulk dielectric constant of the solvent (bulk electrostatic contributions) and the contributions related to other effects (non‐bulk‐electrostatic contributions). The values of non‐bulk‐electrostatic contributions to ΔΔHand ΔΔSsupported the suggestion that these contributions are mainly related to protein‐solvent hyd

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200105

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractThe spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200–320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first‐approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in s

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200106

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractThe conformation and dynamic structure of single‐stranded poly(inosinic acid), poly(I), in aqueous solution at neutral pH have been investigated by nmr of four nuclei at different frequencies:1H (90 and 250 MHz),2H (13.8 MHz),13C (75.4 MHz), and31P (36.4 and 111.6 MHz). Measurements of the proton‐proton coupling constants and of the1H and13C chemical shifts versus temperature show that the ribose is flexible and that base‐base stacking is not very significant for concentrations varying from 0.04 to 0.10Min the monomer unit. On the other hand, the protonT1ratios between the sugar protons,T1(H1′)/T1(H3′), indicate a predominance of theantiorientation of the base around the glycosidic bond. The local motions of the ribose and the base were studied at different temperatures by measurements of nuclear Overhauser enhancement (NOE) of protonated carbons, the ratio of the proton relaxation times measured at two frequencies (90 and 250 MHz), and the deuterium quadrupolar transverse relaxation timeT2. For a given temperature between 22 and 62°C, the13C‐{1H} NOE value is practically the same for seven protonated carbons (C2, C8, C1′, C2′, C3′, C4′, C5′). This is also true for theT1ratio of the corresponding protons. Thus, the motion of the ribose–base unit can be considered as isotropic and characterized by a single correlation time, τc, for all protons and carbons. The τcvalues determined from either the13C‐{1H} NOE or protonT1ratios,T1(90 MHz)/T1(250 MHz), and/or deuterium transverse relaxation timeT2agree well. The molecular motion of the sugar‐phosphate backbone (O‐P‐O) and the chemical‐shift anisotropy (CSA) were deduced fromT1(31P) and31P‐{1H} NOE measurements at two frequencies. The CSA contribution to the phosphorus relaxation is about 12% at 36.4 MHz and 72% at 111.6 MHz, corresponding to a value of 118 ppm for the CSA (σ = σ∥ − σ⟂). Activation energies of 2–6 kcal/mol for the motion of the ribose–base unit and the sugarphosphate backbone were evalu

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200107

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractThe kinetics of a conformational change which occurs in nucleosome core particles at about 1 mMionic strength have been studied by observing changes in the fluorescence of labeled histone H3. The unfolding reaction is intramolecular since no concentration dependence is observed. However, the kinetics are unexpectedly complicated and reveal evidence of at least three relaxation times. It is possible to fit the kinetics observed under several conditions to a consistent four‐state cyclic mechanism in which folded and unfolded forms can inter‐convert by two parallel pathways, each involving a distinct intermediate. While the data are not sufficient to establish this mechanism as a unique choice, they exclude many simpler possibilities. The cyclic mechanism is quite reasonable in view of what is currently known about the structures of the folded and unfolded fo

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200108

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractThe translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well‐known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulate

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200109

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractThe pKaof 3,8‐diamino‐6‐phenyl‐phenanthridine (DAPP), a nonquaternary analog of ethidium bromide, has been determined spectrophotometrically as a function of sodium ion concentration both free in solution and complexed to DNA. Unwinding angle determinations with this compound were determined with Col El DNA using ethidium bromide as a standard. The unwinding angle for DAPP was 24 ± 2° relative to 26° for ethidium, and this suggests that DAPP binds in a manner quite similar to ethidium and with no significant outside bound DAPP under these experimental conditions. Isobestic behavior was obtained on spectrophotometric pH titration above pH 5 as long as the ratio of DNA‐phosphate to ligand was between 100 and 300 and the DNA phosphate concentration was approximately 0.01Mor greater. The loss of isosbestic behavior which occurred below pH 5 is probably due to titration of the 8 amino group of the ligand complexed to DNA. To circumvent this problem, pKavalues and the extinction coefficient of the acidic species were both determined by a computer program using experimental data obtained above pH 5. The pKaof the free compound has only a minor dependence on ionic strength, while the pKaof the ligand bound to DNA in an intercalated complex depends strongly on the sodium ion concentration. The pKaof the DAPP‐DNA complex is a linear function of –log[Na+] as predicted by the ion‐condensation theory of polyelectrolytes. It was determined that DAPP is essentially completely bound to DNA under the conditions of these experiments by (1) determination of apparent pKavalues as a function of total DNA concentration, (2) calculation of binding constants for the neutral species of DAPP, and (3) spectral analysis of the protonated and neutral species of DAPP bound to DNA relative to DAPP free in solution. These results support the ion‐condensation theory; provide an independent method for measuring ψ*, the average number of counterions associated per phosphate of DNA in the intercalated conformation; and illustrate that there are no specific pH effects or absolute pKavalues for ligands bound to DNA, but only ionic‐str

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200110

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY

摘要:

AbstractPhoton‐correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis wereE. colitRNA 2Gluand yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1Mionic strength at 22°C, the equilibrium constants vary from 1 × 105M−1in the absence of magnesium to 1.5 × 106M−1in 10 mMMg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔHand ΔScontribute to the free energy of binding and that their relative contributions are similar for each solution conditi

ISSN:0006-3525    

DOI:10.1002/bip.1981.360200111

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1981

数据来源: WILEY