摘要:

AbstractBinding isotherms for acridine orange (AO)–heparin systems can be evaluated solely on the basis of quantitative fluorescence spectroscopic measurements. The evaluation of thermodynamic parameters indicates that the interactions of AO with heparins from several animal sources are similar to each other in magnitude. Binding is highly exothermic (ΔH= −6 kcal mol−1) and is stabilized by dye–polymer and dye–dye (coopertive) interactions, as well as by entropic factors (ΔS= +7 e.u.). The predominant stabilizing factor appears to be the electrostatic attraction between the AO cation and the heparin polyanion, although the other factors are important as well. At 24°C the value of the cooperative binding constants for the various heparins range from 8.8 to 11.3 × 105M−1, corresponding to a free energy of −8 kcal mol−1. The degree of cooperativity, which is a direct measure of dye–dye interaction, varies with polymer:dye ratio; the theoretical basis for this variation remains to be elucidated. Electrophoretic data indicate that each heparin sample consists of a mixture of species, each with its own charge density. This precludes definitive interpretation of observed small differences in the values of the thermodynamic parameters among the various samples until each sample can be resolve

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180302

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

年代:1979

数据来源: WILEY

摘要:

AbstractThe far‐ir absorption spectrum of lysozyme was measured at room and liquid‐nitrogen temperatures. Dried layers of single crystals of tetragonal lysozyme chloride with a diameter of 100–300 μm were grown on a silicon plate. Such single‐crystalline samples were considered to have the following advantages in obtaining far‐ir spectra: (1) surface scattering is reduced, (2) the protein molecules are closely packed, and (3) air‐drying of the crystals reduces the number of water molecules without considerably changing the original configuration. The spectrum obtained consisted of a strong background absorption and a number of absorption peaks that were not clearly observed with the sample in the form of lyophilized powder. The peaks were ascribed to various delocalized vibrations of the main and side chains in the molecule. The peaks were also compared with the positions of Raman lines. The uniform background was assigned to the water molecules remaining in

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180303

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

年代:1979

数据来源: WILEY

摘要:

AbstractC24H34N2O9, orthorhombic, P212121;a= 39.432 (10),b= 14.061 (5),c= 4.850 (2) Å,M= 494 a.m.u.,Z= 4,Dm= 1.22 g cm−3,Dx= 1.22 g cm−3,R= 0.13 for 1205 observed reflections after refinement with isotropic thermal factors. The urethane and amide bonds are in thetransconfiguration, as well as all the ester groups. The φ and ψ angles of theL‐glutamyl residues fall in the β‐structure region of the Ramachandran's plot; the molecule is rather flat with the amide plane almost parallel to thecaxis along which two hydrogen bonds hold the molecules together to form long rows in a “parallel pleated

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180304

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

年代:1979

数据来源: WILEY

摘要:

AbstractA series of proline‐containing linear oligopeptides (4 dipeptides and 15 tripeptides) were synthesized and examined in aqueous and nonaqueous solutions using13C‐nmr spectroscopy. Spectra of linear tripeptides showingcis‐transisomerism about theX‐Pro bond (X= Pro, Gly, and Ala) also show neighboring effects on the chemical shifts of residues both preceding and following the prolyl moiety. The extent ofcis‐transisomerism observed about theX‐Pro peptide bond correlates not only with the nature ofX, but also depends on the size of the residue following proline; the larger substituents favor an increase inciscontent about th

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180305

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

年代:1979

数据来源: WILEY

摘要:

AbstractThe three‐dimensional structure of putrescine diphosphate has been solved by x‐ray diffraction analysis. The structure reveals the detailed interaction between the amino groups of putrescine and the phosphate residues in which hydrogen bonding and electrostatic forces play a predominant role. The structure serves as a useful model for understanding the interaction of amines with nucleic acids both in a sequence‐specific and non‐sequence‐specific fashion. In particular, a model is proposed for the interaction of the E‐amino group of lysine with regions of DNA containing adenine–thym

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180306

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

年代:1979

数据来源: WILEY

摘要:

AbstractThe duplex‐to‐strand transition of the self‐complementary sequence dG‐dC‐dG‐dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high‐resolution nmr spectroscopy. The Watson‐Crick imino and amino hydrogen‐bonded protons, as well as the exposed amino protons, could be followed through the duplex‐to‐strand transition and provide information on base‐pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base‐proton chemical shifts on duplex formation are consistent with calculations based on base‐pair overlap geometries of the B‐DNA type. The variation of the31P chemical shifts in dG‐dC‐dG‐dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the OP bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG‐dC‐dG‐dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercala

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180307

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

年代:1979

数据来源: WILEY

摘要:

AbstractPossible conformations of the disaccharide–peptide subunit of peptidoglycan (ofStaphylococcus aureusorMicrococcus luteus) have been studied by an energy‐minimization procedure. The favored conformation of the disaccharideN‐acetyl‐glucosaminyl‐β(1–4)‐N‐acetylmuramic acid (NAG‐NAM) is different from that of cellulose or chitin; this disagrees with the assumption of earlier workers. The disaccharide–peptide subunit favors three types of conformations, among which two are compact and the third is extended. All these conformations are stabilized by intramolecular hydrogen bonds. Based on these conformations of the subunit, two different models are proposed for the three‐dimensional arrangement of peptidoglycan in t

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180308

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

年代:1979

数据来源: WILEY

摘要:

AbstractConformational analyses of cyclic tetrapeptides consisting of alternatingcisandtranspeptide units have been made using contact criteria and energy calculations. This study has been restricted to those structures having a symmetry element in the backbone ring, such as a twofold axis (d) or a center of inversion (i). There are five main results. (1) There are twodistincttypes of conformations, which are stereochemically favorable corresponding to each of twofold and inversion‐symmetrical structures, designated asd1,d2(for twofold symmetrical) andi1,i2(for inversion‐symmetrical). Among these, thei1type has the lowest energy when glycyl residues occur at all four α‐carbon atoms. (2) With the glycyl residue at all four α‐carbon atoms, methyl substitution at thecispeptide nitrogen atoms is possible in all the four types, whereas the substitution attranspeptide nitrogen atoms is possible only for thei1type. Thus only in thei1type can all the nitrogen atoms be methylated simultaneously. The conformation of the molecule in the crystal structure of cyclotetrasarcosyl belongs to thei1type. (3) When alanyl residues occur at all four α‐carbon atoms, the possible symmetrical type is dependent on the enantiomorphic form and the actual sequence of the alanyl residues. (4) The methyl substitution at peptide nitrogen atoms for cyclic tetrapeptides having alanyl residues causes more stereochemical restriction in the allowed conformations than with glycyl residues. (5) The prolyl residue can be incorporated favorably at thecis‐transjunction of bothdanditypes of structures. The results of the present study are compared with the data on cyclic tetrapeptides available from the crystal structure and nmr studies. The results show an overall agreement both regarding the type of symmetry and the conformatio

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180309

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

年代:1979

数据来源: WILEY

摘要:

AbstractA general model for the large‐scale, time‐independent structure of duplex DNA is developed based on elastic considerations. The general conditions of elastic equilibrium are given. These equations are solved for the equilibrium shape of stressed duplex DNA, based on the assumption that the double helix behaves mechanically as a symmetric, linearly elastic rod. It is shown that, in general, two orders of superhelicity will arise at equilibrium. Several possible applications of this approach to the supercoiling of closed circular DNA are descri

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180310

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

年代:1979

数据来源: WILEY

摘要:

AbstractBased on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ions with atoms N(7)of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7)and O of C(6)of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequencedGpC. CD spectra of the resulting nondenatured complex (DNA–Cu2+)natmay be interpreted in terms of a conformational change of DNA from the B‐form to a C‐like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA–Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ions to atoms N(3)of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ions between atoms N(7)and O of C(6)of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence‐specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ions with DNA.In temperature‐jump experiments with the nondenatured complex (DNA–Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex format

ISSN:0006-3525    

DOI:10.1002/bip.1979.360180311

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

年代:1979

数据来源: WILEY