ISSN:0006-3525    

DOI:10.1002/bip.360250802

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

年代:1986

数据来源: WILEY

摘要:

AbstractApo‐ and holo‐forms of horse liver alcohol dehydrogenase (LADH) in solution were studied by diffuse x‐ray scattering. Experimental scattering curves for apo‐ and holo‐forms coincide both with the curves calculated from the crystal structures of apo‐ and holo‐enzymes, and with each other. Thus the “sliding” of catalytical domains in LADH upon substrate binding, which has been shown by x‐ray analysis, cannot be detected by diffuse x‐ray scattering. Sensitivity of the scattering curves to the domain displacements of sliding and “locking” types has been investigated. It has been shown that the scattering curves of LADH are rather sensitive to the domain “unlocking.” However, these curves change only slightly upon sliding of domains, including the sliding of domains obser

ISSN:0006-3525    

DOI:10.1002/bip.360250803

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe three‐dimensional structure was determined by x‐ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having thecis‐syncyclobutane (CB) geometry and the S‐configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121(Z = 4), with cell dimensionsa= 11.596 Å,b= 14.834 Å, andc= 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T:Q: 0.24 Å (0.31 Å); θ: 123° (120°); ϕ: 141° (86°). These represent half‐chairs designated as6H1(T[p]) and6H5([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p]segment has thesynglycosyl conformation, a2T3sugar pucker, andgauche−conformation at C4′‐C5′; the [p]T segment isanti,3T4,trans. The C5′‐O5′ torsion of the [p]T unit is –124.5°, and the C3′‐O3′ torsion of the T[p]unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P‐O3′ and P‐05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecul

ISSN:0006-3525    

DOI:10.1002/bip.360250804

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe CD and absorption (OD) spectra of single‐stranded nucleic acids in complex with the helix‐destabilizing protein of either bacteriophage T4 (GP32) or bacteriophage fd (GP5) show similar and unusual features for all polynucleotides investigated. The change in the CD spectra between 310 and 240 nm is in all cases characterized by a considerable decrease in the positive band, while the negative band (if present) remains relatively intense. These changes are different from those due to temperature or solvent denaturation and, moreover, cannot be induced by the binding of simple oligopeptides. Absorption measurements show that all polynucleotides remain hypochromic in the complex. Both CD and OD spectra point to a specific and probably similar conformation in complex for all polynucleotides with substantial interactions between the bases. The spectral properties are almost temperature independent (0–40°C). Therefore, we conclude that the conformation must be regular and rigid. To investigate the relation between these optical properties and the specific polynucleotide structure, CD and OD spectra were calculated for an adenine hexamer over a wide range of the conformational parameters. It appears that the calculated CD intensity is not very sensitive to an increase in the axial increment and that many different conformations can give rise to more or less similar CD spectra. However, simulation of the very nonconservative experimental CD spectrum of the poly(rA)‐GP32 complex requires that the conformation satisfies two criteria: (1) a considerable tilt of the bases (≲ – 10°) in combination with (2) a small rotation per base (≃20°) and/or a position of the bases close to the helix axis (dx ≃ 0 Å). Such conformations can also explain the observed hyperchromism upon binding of GP32 to poly(rA)/(dA). Very similar structural characteristics also account for the optical properties of the complexes with GP5. These are discussed as an alternative to the structure suggested by Alma‐Zeestraten for poly(dA) in the complex [N. C. M. Alma‐Zeestraten (1982) Doctoral thesis Catholic University, Nijmegen, The Netherlands]. The secondary structure proposed in this work can be reconciled with the overall dimensions of the complex, assuming that the polynucleotide helix is further or

ISSN:0006-3525    

DOI:10.1002/bip.360250805

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe ability of residues of type Y to disrupt the helix formed by residues of type X has been studied in X‐Y‐X‐block copolypeptides. The degree of polymerization of each X‐block is so large that it can be considered to be infinite. Matrix methods are used to obtain a general expression for the helix content of the central residue in the Y‐block. The resulting expression is specialized to the case where the statistical‐weight matrix is of dimensions 2 × 2, with elements, 1, 1, σs, ands. The behavior is evaluated for physically realistic values of σ ands. Two useful generalizations emerge: (1) The ability of the Y‐block to disrupt the helix is determined primarily by the value ofsfor residues of type Y. Helix disruption does not correlate well with the helix content of a Y‐homopolymer of infinite degree of polymerization. (2) In contrast, the ability of the X‐block to resist the influence of the Y‐block is determined primarily by the helix content of the X‐block. It does not correlate well withsfor residues of type X. A random‐coil region in a Y‐block that continues into the following X‐block is more stable if residues of type X have a large value of σ because there is helix initiation in the X‐block. It is this influence of σ that prevents a correlation betweensand the ability of the X‐block to resist the

ISSN:0006-3525    

DOI:10.1002/bip.360250806

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

年代:1986

数据来源: WILEY

摘要:

AbstractNew adenine (A) and uracil (U) π → π* transition‐moment parameters have been derived from a recently developed semiempirical procedure. Using conformational energy probabilities based on the Boltzmann equation, the new parameters were assigned by optimizing the calculated CD of cyclic nucleotides against measured CD. The derived A‐and U‐parameters (along with guanine and cytosine parameters derived previously by the same procedure) have been assessed in CD spectral calculations of some polyribonucleic acid sequences, in assumed A‐class geometries. Comparisons have been made between CD spectra calculated from the newly derived parameters and those calculated from parameters obtained from a combination of crystal optical measurements and quantum‐mechanical calculations. Although some spectral differences do occur, for the RNA sequences considered, no major disagreements were found in CD spectral signs and shapes, between measurements and calculations. Overall, the results indicate that the newly derived A‐, U‐, G‐, and C‐parameters show better agreement between theory and experiment than those used in previous nucleic

ISSN:0006-3525    

DOI:10.1002/bip.360250807

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe conformation of melittin, a surface‐active polypeptide, in solution was studied by CD spectra between 190 and 240 nm. The molecule was essentially unordered (possibly with a trace of helix) in water without salt at neutral pH. Upon deprotonation of four of the six cationic groups at pH 12 the polypeptide became partially helical (about 35%). The addition of NaDodSO4to an aqueous melittin solution first caused the solution to become turbid but it became clear again in excess surfactant solution. The conformational changes depended on the molar NaDodSO4/melittin ratio,R. WithRfrom 2.34 to 23.4, the melittin solution was turbid and the polypeptide conformation was probably a mixture of α‐helix and β‐sheets. This was supported by the ir spectrum of the turbid solution, which indicated the presence of both conformations. WithR= 46.8 or 468 (1 or 10 mMNaDodSO4) the polypeptide conformation was characteristic of an α‐helix, about 70–80% of the molecule, regardless of whether the surfactant was above or below its critical micelle concentration. This compared well with the x‐ray results of 92% helix in crystals. The lower helicity of melittin in NaDodSO4solution might be attributed to the end effects that destabilize the first and last turn of an helix at its N‐ and C‐term

ISSN:0006-3525    

DOI:10.1002/bip.360250808

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

年代:1986

数据来源: WILEY

摘要:

AbstractLight‐scattering techniques have been used to measure the z‐average radius of gyrationRgz‐average translational diffusion coefficientDtand weight–average molecular weightMwof porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has aMwabout twice as large as a sample prepared without these precautions. The former sample has aMwof 17 × 106in 0.1MNaCl, which decreases to 8 × 106in 6Mguanidine hydrochloride (GdnHCl) and then to 2 × 106on addition of 0.1Mmercaptoethanol to the 6MGdnHCl solution. TheRgorD −1tvalues obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log–log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligos

ISSN:0006-3525    

DOI:10.1002/bip.360250809

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

年代:1986

数据来源: WILEY

摘要:

AbstractWe have studied aggregation/association of monodisperse DNA fragments (ranging from 30–90 base pairs) by steady‐state fluorescence polarization of intercalculated ethidium. The method of excitation at different wavelengths in the ethidium absorption spectrum provides information about anisotropic twisting and tumbling mobility of the fragments. We find that end‐over‐end tumbling rather than axial spinning and internal twisting motions are affected by aggregation/association. The critical concentration for observing the effects of intermolecular interactions is approximately 5 mg DNA/mL at room temperature, independent of fragment length. Association is favored by low temperature and high (>10 mM) concentration of Mg2+. From temperature‐and salt‐dependence experiments we infer that the “aggregates” are similar to those observed in a recently discovered DNA sol–gel transition [M. G. Fried and V. A. Bloomfield (1984)Biopolymers23, 2141–2155]. We also discuss possible arrangements of the fragments within the aggregates and their possible relation to formation of

ISSN:0006-3525    

DOI:10.1002/bip.360250810

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B‐DNA) and also in 80% ethanolic solution (A‐DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A‐DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary struc

ISSN:0006-3525    

DOI:10.1002/bip.360250811

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

年代:1986

数据来源: WILEY