摘要:

AbstractThe coil–helix transition has been studied for alkali metal salts of poly (L‐glutamic acid) (PLG), i.e., PLGLi, ‐Na, ‐K, and ‐Cs, in aqueous organic solvent systems. Dependence of the transition on the solvent composition has been qualitatively discussed in terms of the solvent dielectric constantD, Gutmann's acceptor number AN, and water activityaw. The helix formation induced by addition of alkali chlorides has also been studied. The sharpness of the transition has been interpreted as a measure of reduction of electrostatic energy of helical PLG through contact ion‐pair formation between a counterion and car

ISSN:0006-3525    

DOI:10.1002/bip.360310102

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe permeability of bacteriophage T4 and the change in T4 permeability caused by mutation to osmotic shock resistance are investigated here by quantification of the kinetics with which both a DNA‐specific probe (ethidium) and a protein‐specific probe [1,1′‐bi(4‐anilino) naphthalene‐5,5′‐di‐sulfonic acid, or bis‐ANS] bind to T4. In the case of an osmotic shock‐resistant mutant, T40s41, both ethidium and bis‐ANS bind with first order kinetics. The first‐order rate constant (k*) for both bis‐ANS and ethidium is a function of anion type and concentration. Adenosine triphosphate, phosphate, bisulfite, sulfate, and acetate anions all reducek* below thek* observed when chloride is the only anion. When chloride is the only anion at 25°C,k* values for binding to T40s41 are orders of magnitude abovek* values for binding to wild‐type T4 (T4wt). At 25°C,k* forT4wt is too small to measure, butk* for T4wt increases at 50–55°C to values approaching those measured for T40s41, without inactivating T4wt, when chloride is the only anion; during heating, T4wt is stabilized by both ethidium and bis‐ANS. Binding to T4wt is reversible at 50‐55°C, but not at 25°C. Equilibrium binding of bis‐ANS to T40s41 reveals 112 ± 24 sites per T4 capsid. Equilibrium binding of ethidium to T40s41 reveals both high‐ and low‐affinity sites previously observed in the packaged DNA of other bacteriophages. The ATP‐induced decrease ink* is not accompanied by a decrease in equilibrium binding. The following hypotheses are presented to explain the above data: (a) All detected bis‐ANS binding sites on T4 are interior to the outer surface of T4. (b) The value ofk* for both bis‐ANS and ethidium is controlled at the port(s) of passage through the outer shell of the T4 capsid. (c) The anions present controlk* values at the port(s) of entry, probably by controlling the size of this port. The effects onk* of phosphate explain the otherwise paradoxical observation [P. J. McCall and V. A. Bloomfield (1976)Biopolymers15, 2323–2336] that in a phosphate bu

ISSN:0006-3525    

DOI:10.1002/bip.360310103

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe adjacent GN7‐M‐GN7 cross‐linking and adjacent G‐M‐G sandwich‐complex models for DNA metal ion binding were evaluated both with native DNAs differing in GC content as well as with the synthetic polymers poly[(dGdC)]2, poly[(dAdT)]2, and poly[(dAdC)(dGdT)]. The effect of Zn2+was studied in depth, and limited studies were also performed with Co2+and Mg2+. The results were compared to the extensive information available on Cu2+binding to native DNAs and poly [(dAdT)]2. At high ratios of metal/base (R), Zn2+caused all native DNAs to denature with the same melting temperatureTm, ∼ 61°C. A similar pattern was reported previously for Cu2+, but the typicalTm, was ∼ 35°C. The extent of renaturation on cooling DNAs denatured in the presence of Zn2+increased with GC content, as reported previously for Cu2+. These results, together with previously reported similarities, strongly indicate that the DNA binding characteristics of the two cations are similar. By comparison of theTmvalues and hyperchromicity changes monitored at 260 and 282 nm, it is clear that, during thermal denaturation in the presence of Zn2+, both AT and GC regions were denatured, even at highR. TheTmvsRprofile for the native DNAs was typical. The rise at lowRand subsequent decrease at highRwere inversely and directly related, respectively, to GC content. Except for poly[(dAdT)]2, whereTm, increased withR, the other synthetic polymers exhibited the increase/decrease pattern. Poly[(dAdC)(dGdT)] gave aTm, value a at highRof 54°C. In the absence of Zn2+, this polymer exhibited little hypochromicity on cooling of denatured polymer. However, in the presence of Zn2+, nearly complete hypochromicity was observed, although the midpoint of the cooling curve was lower than theTmvalue by ∼ 15°C atR= 10. These characteristics were similar to those with native DNAs, although viscosity and CD studies suggested that the “renatured” polymer was not identical to the unheated polymer. Furthermore, addition of Zn2+after denaturation nearly completely reversed the absorption increase. This finding contrasts with those for native DNAs, where the Zn2+must be present during denaturation in order to reverse the absorption increase nearly completely on cooling. With some caveats, poly[(dAdC)(dGdT)] appears to be a good model for native DNAs since its properties, including CD and uv changes on addition of Zn2+to premelted and melted polymer, parallel those of the native polymers. Based on these findings and the discovery that Zn2+actually inhibits renaturation of poly[(dGdC)]2, we believe adjacent G‐M‐G complexes are not the primary species responsible for the spectral changes in pre‐ melted DNAs, nor are they the principal species promoting renaturation. Three interrelated hypotheses to explain these phenomena were identified for further study as follows: (a) a kinetic effect–the metal ion promotes renaturation of denatured regions formed during thermal denaturation with metal ion present; (b) an inhibiting effect–the metal ion prevents the initial formation of conformations that otherwise inhibit renaturation; and (c) a CN3 binding effect–the metal ion lowersTmby stabilizing the denatured state through C binding. We speculate that such CN3 binding may account for the unexpectedly poor ability of Co2+both

ISSN:0006-3525    

DOI:10.1002/bip.360310104

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

年代:1991

数据来源: WILEY

摘要:

AbstractHeteronuclear multispin coherence proton‐detected two‐dimensional nmr spectroscopic experiments were used to obtain information on protonated carbons and nitrogens of the self‐complementary d (G‐G‐T‐A‐T‐A‐C‐C) and d (G‐G‐A‐A‐T‐T‐C‐C) duplexes, with and without the drug netropsin dissolved in aqueous solution. Many correlations of protons coupled to13C nuclei on the base and sugar rings of the octanucleotides were detected, allowing the carbon resonances to be assigned based on previous homonuclear proton two‐dimensional nmr studies. Imino nitrogen assignments can also be made using the proton assignments from previous one‐dimensional nuclear overhauser effect experiments. Imino nitrogen shifts may be useful indicators of changes in local hydrogen‐

ISSN:0006-3525    

DOI:10.1002/bip.360310105

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe starch–iodine blue complex formation does not involve negatively charged iodine species like I 3−, I 5−, or I 7−; rather, neutral iodine units are involved. The heat of reaction is determined to be about −110 kJ for every mole of I‐I unit in the amylose helix, which suggests that the dissociation of I2(binding energy 149 kJ/mol) does not take place during the complex formation. Quantum mechanical (INDO CI) calculations indicate that the linear as well as nonlinear polyiodine units, I6, with interiodine distance of 3.0 Å are responsible for characteristic absorbance bands of the starch–iodine complex. Based on our previous article [(1989)J. Polym. Sci. A27, 4161] and the present studies we identify (C6H10O5)16.5I6to be the polymeric unit responsible for the characteristic blue

ISSN:0006-3525    

DOI:10.1002/bip.360310106

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

年代:1991

数据来源: WILEY

摘要:

AbstractPolyriboadenylates of alkali metals were obtained from (1) K+‐poly(A) (salts I) and (2) H+‐poly( A) (salts II) by the ion‐exchange method. The conductivity of these salts as well as of H+‐poly(A) were studied. Salts I and II of the same counterion were shown to have significantly different conductivity coefficients (f) and polyion conductances (λ p0). The charge density parameter (ζ) was 1.3 and 2.5, respectively, with λ p0equal to 44 and 83 ohm−1cm2mole−1for poly(A)‐I and poly (A)‐II salts, respectively. This is credited to the difference in the conformations of corresponding polyions. The linear dependence of equivalent conductivity on the square root of polymer concentration (Kohlrausch coordinates), earlier obtained for DNA, is also satisfied for the studied polynucleotides. A comparison of the slopes of straight lines in Kohlrausch coordinates for poly(A), simple electrolytes, and for earlier studied polyribouridylic acid salts lends credence to the concepts, developed by a number of authors, that DNA can act as a “buffer” against the ion–ion interaction in concentrated electrolyte solutions. Using the approximation that the polyion conductance is independent of the counterion nature, parameterf(agreeing in this case with Eisenberg parameter ϕ) has been shown to decrease as the polynucleotide concentration is increased; the decrease is caused by the relaxation effect. The transference numbers of counterions, which have negative values in poly (A)‐II solutions, grow with the increase in polymer concentration; the higher the ζ, the more apparent is this increase. This is explained by the increase in the fraction of conductivity along the polyion chains (“surface” conductivity) with the gro

ISSN:0006-3525    

DOI:10.1002/bip.360310107

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

年代:1991

数据来源: WILEY

摘要:

AbstractAn important direction in biological simulations is the development of methods that permit the study of larger systems and/or longer simulation time scales than is currently feasible by molecular dynamics. One such method designed with this objective in mind is stochastic boundary molecular dynamics (SBMD). SBMD was developed for the characterization of spatially localized processes in proteins, and has been shown to successfully reproduce structural and dynamical properties of these macromolecules, as compared to a molecular dynamics control simulation, when concerted or global motions arenotpresent. The virtual rigid body dynamics method presented in this work extends the range of applicability of the SBMD method, by providing a framework to include these important long time scale conformational transitions. In this paper we describe the two‐step implementation of the virtual rigid body model: first, the reduction of the full atomic representation to a reduced particle (virtual bond) model, and second, the propagation of the dynamics of flexibly connected rigid bodies containing virtual atom site

ISSN:0006-3525    

DOI:10.1002/bip.360310108

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe interaction of guanosine‐5′‐monophosphoric acid (H2‐GMP) with the alkaline earth metal ions has been studied in aqueous solution at neutral pH. The crystalline salts of the type Mg‐GMP·5H2O, Ca‐GMP·6H2O, Sr‐GMP·7H2O, and Ba‐GMP·7H2O were isolated and characterized by Fourier transform ir,1H‐nmr and x‐ray powder diffraction measurements. Two types of macrochelate complexes have been identified: (a) The direct metal–base and indirect metal–phosphate bindings (inner and outer sphere interaction) for the Mg(II), Ca(II), and Sr(II), ions; and (b) the indirect metal–base and direct metal–phosphate bindings (outer and inner sphere interaction) for the Ba(II) ion. In aqueous solution, an equilibrium exists between the base–metal–H2O…PO3and base … H2O–M–PO3interactions. The ribose moiety shows C3′‐endo/anticonformation in the free acid; C2′‐endo/antiin the Na2‐GMP salt; C3′‐endo/antiin the Mg(II)‐, Ca(II)‐, an

ISSN:0006-3525    

DOI:10.1002/bip.360310109

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

年代:1991

数据来源: WILEY

摘要:

AbstractIn order to characterize the first step of agarose gelation, highly dilute solutions (2·10−3to 0.5 g/L) have been studied by means of the transient electric birefringence technique. The field‐free decay curves of the birefringence are well described by a stretched‐exponentialB(t) ≈ exp(−t/τ)β; the value of the exponent β is close to 0.5 whatever the agarose concentration. The suspended particles observed by electron microscopy present a rod‐like shape with a constant diameter (∼50 Å), without any branching; they are polydisperse with a distribution of lengths approximately exponential. The mean length of these fibers, deduced from their mean rotational diffusion coefficient, is proportional to the 0.37 power of the agarose concentration in the solution. Furthermore, these particles possess a strong permanent electrical dipole confirming the side‐to‐side arrangement of helices into bundles; this dipole is roughly proportional to the particle length, indicating a self‐similarity in the unidirectional growth of the agarose fibers, even when approaching t

ISSN:0006-3525    

DOI:10.1002/bip.360310110

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

年代:1991

数据来源: WILEY

摘要:

AbstractBinding of the hydrophobia fluorescent probe, 1‐anilino‐naphthalene‐8‐sulfonate (ANS), to synthetic polypeptides and proteins with a different structural organization has been studied. It has been shown that ANS has a much stronger affinity to the protein “molten globule” state, with a pronounced secondary structure and compactness, but without a tightly packed tertiary structure as compared with its affinity to the native and coil‐like proteins, or to coil‐like, α‐helical, or β‐structural hydrophilic homopolypeptides.The possibility of using ANS for the study of equilibrium and kinetic molten globule intermediates is demonstrated, with carbonic anhydrase, β‐lactamase, and

ISSN:0006-3525    

DOI:10.1002/bip.360310111

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

年代:1991

数据来源: WILEY