摘要:

AbstractInterest in the thermodynamics of the iron‐binding site in hemoproteins has increased in recent years due to refinements in x‐ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M.&Moffat, K. (1976)J. Mol. Biol.104, 687–706; Heidner, E. J., Ladner, R. C.&Perutz, M. F. (1976)J. Mol. Biol.104, 707–722; Deathage, J. F., Lee, R. S.&Moffat, K. (1976)J. Mol. Biol.104, 723–728; Ladner, R. C., Heidner, E. J.&Perutz, M. F. (1976)J. Mol. Biol.114, 385–414; Fermi, G.&Perutz, M. F. (1977)J. Mol. Biol.114, 421–431; Takano, T. (1977)J. Mol. Biol.110, 537–568 and 569–589], the synthesis and x‐ray analysis of model heme compounds [see Scheidt, W. R. (1977)Acc. Chem. Res.10, 339–345; Kastner, M. E., Scheidt, W. R., Mashino, T.&Reed, C. A. (1978)J. Am. Chem. Soc.100, 666–667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R.&Reed, C. A. (1978)J. Am. Chem. Soc.100, 6354–6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K.&Pellizer, G. (1979)Chem. Commun.4, 151–152; and Scheidt, W. R., Cohen, I. A.&Kastner, M. E. (1979)Biochemistry18, 3546–3556], and the numerous data on heme–protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T.&Yonetani, T. (1970)Adv. Biophys.1, 157–182; Smith, D. W.&Williams, R. J. P. (1970)Struct. Bond.7, 1–45; and Spiro, T. G. (1975)

ISSN:0006-3525    

DOI:10.1002/bip.360230702

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

年代:1984

数据来源: WILEY

摘要:

AbstractA linear relationship in each of the torsion angle pairs, α‐β, β‐ϵ, ϵ‐ζ, and α‐γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C.&Tinoco, I., Jr. (1968)Biopolymers6, 223–242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand se

ISSN:0006-3525    

DOI:10.1002/bip.360230703

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

年代:1984

数据来源: WILEY

摘要:

AbstractWe have used Brillouin scattering to determine the speed of sound in (and hence longitudinal modulus of) A‐ and B‐DNA fibers. The speed of sound is very sensitive to the degree of hydration of the fibers, and measurements have to be made at laser powers below 5 mW to avoid local heating and dehydration. Under those conditions, we obtain sound speed perpendicular to the fiber axis of about 2.2 and 1.9 km/s in A‐ and B‐DNA fibers, respectively. A‐DNA fibers show a small anisotropy with sound speeds along the fiber axis higher by up to 10% B‐DNA fibers appear to b

ISSN:0006-3525    

DOI:10.1002/bip.360230704

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

年代:1984

数据来源: WILEY

摘要:

AbstractConformational‐energy computations have been carried out for theN‐acetyl‐N′‐methylamides of the Pro‐Pro, Pro‐Gly, and Gly‐Pro dipeptides and of the Pro‐Pro‐Gly‐Pro tetrapeptide, serving as models for the conformational analysis of single‐stranded poly(Gly‐Pro‐Pro). The probability of β‐bend formation for the Pro‐Gly sequence is very high, viz., 0.72 for the terminally blocked Pro‐Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β‐bend conformations of the Pro‐Gly sequence are of low energy in single‐chain poly(Gly‐Pro‐Pro) as well. The β‐bend structure had been postulated earlier to be a requirement for post‐translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β‐bend structure is energetically favorable and hence can be acc

ISSN:0006-3525    

DOI:10.1002/bip.360230705

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

年代:1984

数据来源: WILEY

摘要:

AbstractA method for generating a complete polypeptide backbone structure from a set of Cαcoordinates is presented. Initial trial values of ϕ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual‐bond backbone, e.g., and α‐helical region), and values of ϕ and ψ for the remaining residues (both towards the N‐ and C‐terminus) are then computed, subject to the constraint that the chain have the same virtual‐bond angles and virtual‐bond dihedral angles as the given set of Cαcoordinates. The conversion from Cαcoordinates to full backbone dihedral angles (ϕ,ψ) involves the solution of a set of algebraic equations relating the virtual‐bond angles and virtual‐bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cαcoordinates taken from standard‐geometry full‐atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error‐sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cαcoordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that ϕProbe near −75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean‐square deviation of the calculated Cαcoordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cαcoordinates had an rms deviation of 0.26 Å from t

ISSN:0006-3525    

DOI:10.1002/bip.360230706

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe interaction of magnesium ions with Des‐Trp1‐Nle12‐minigastrin I (Nle11‐HG‐13) and Nle115‐little gastrin I (Nle15‐HG‐17) has been studied by CD and spectrophotometric techniques in trifluoroethanol. Spectrophotometric titrations using murexide as a metallochromic indicator showed that there are three binding sites for magnesium ions in Nle11‐HG‐13, with binding constants of the order of (6 ± 2) × 106, (1.7 ± 0.5) × 106, and (5.0 ± 0.5) × 105M−1. These figures have been independently confirmed by CD measurements in the far‐uv in the presence of increasing amounts of magnesium ions. Elongation of the peptide chain from Nle11‐HG‐13 to Nle15‐HG‐17 does not provide any additional binding site for the metal ions. In both hormones, we have observed different responses in the near‐ and fur‐uv CD properties with regard to added magnesium. The intensity of the CD bands in the aromatic region changes cooperatively with the ion/hormone molar ratio. These findings lead us to conclude that at the C‐terminal, the biologically important sequence, ‐Trp‐Nle‐Asp‐Phe‐Nh2, i

ISSN:0006-3525    

DOI:10.1002/bip.360230707

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe interaction of Cu(II) with the protamine scylliorhinine Z3was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5–6.5, the results suggest the formation of a five‐membered chelate ring through the coordination of two nitrogen atoms, the N‐terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2group of Arg; at pH 6.5–8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)‐Z3solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge‐transfer dichroic band transitions. At Cu(II):Z3molar ratios ≥ 2 and at pH>8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in m

ISSN:0006-3525    

DOI:10.1002/bip.360230708

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

年代:1984

数据来源: WILEY

摘要:

AbstractWe consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one‐dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of lengthn. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983)Biopolymers22, 1697–1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n−2) internal positions of ann‐cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero‐order dissociation kinetics predicted by the Loh

ISSN:0006-3525    

DOI:10.1002/bip.360230709

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

年代:1984

数据来源: WILEY

摘要:

AbstractStudies of the optical birefringence of solutions of acid‐soluble collagen from rat‐tail tendon at 22°C in the pH range 1.0–6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt‐soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the m

ISSN:0006-3525    

DOI:10.1002/bip.360230710

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe P‐Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P‐form has little or no hydrogen bonding, while the data from EM show that the P‐form has a condensed tertiary structure. In earlier work, we demonstrated that the P‐form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P‐Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P‐form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non‐hydrogen‐bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P‐form that h

ISSN:0006-3525    

DOI:10.1002/bip.360230711

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

年代:1984

数据来源: WILEY