摘要:

AbstractFiveN‐protected tetrapeptide esters of the structure Gly‐Pro‐X‐X*‐O‐methyl were synthesized in such a way that one of the two variable amino acid residues (X) was isotopically enriched in15N (denoted by*). The variable amino acids are glycine, alanine, leucine, valine, and phenylalanine. For the natural abundance15N‐nmr spectra of these tetrapeptide derivatives in methylene chloride only the signals of the Gly‐Protransisomer were found. In a 2:1 mixture of acetone and dimethylsulfoxide, signals for both thecisandtransisomers were observed. Three of the five tetrapeptide derivatives showcis/transsplitting of all four nitrogen signals. The15N‐nmr spectra ofZ‐Pro‐Pro‐OH and of (D,L‐proline)nwere measured in a 2:1 mixture of acetone and dimethylsulfoxide as well as in water. The effects of solvents and neighboring residues and the influence of thecis/transisomerism on the nmr spectra are discussed. The determination of thecis/transequilibria and the assignment of the15N‐nmr signals of all oligopeptides were achieved by selective isotopic enrichment and

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190602

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

年代:1980

数据来源: WILEY

摘要:

AbstractPoly(L‐arginine) assumes the α‐helix in the presence of the tetrahedral‐type anions or some polyanions by forming the “ringed‐structure bridge” between guanidinium groups and anions which is stabilized by a pair of hydrogen bonds and electrostatic interaction [Ichimura, S., Mita, K.&Zama, M. (1978)Biopolymers17, 2769–2782; Mita, K., Ichimura, S.&Zama, M. (1978)Biopolymers17, 2783–2798]. This paper describes the parallel CD studies on the conformational effects on poly (L‐homoarginine) of various mono‐, di‐, polyvalent anions and some polyanions, as well as alcohol and sodium dodecylsulfate. The random coil to α‐helix transition of poly(L‐homoarginine) occurred only in NaClO4solution or in the presence of high content of ethanol or methanol. The divalent and polyvalent anions of the tetrahedral type (SO 42−, HPO 42−, and P2O 74−), which are strong α‐helix‐forming agents for poly(L‐arginine), failed to induce the α‐helical conformation of poly(L‐homoarginine). By complexing with poly(L‐glutamic acid) or with polyacrylate, which is also a strong α‐helix‐forming agent for poly(L‐arginine), poly(L‐homoarginine) only partially formed the α‐helical conformation. Monovalent anions (OH−, Cl−, F−, and H2PO 4−) did not change poly(L‐homoarginine) to the α‐helix, and in the range of pH 2–11, the polypeptide remained in an unordered conformation. In sodium dodecylsulfate, poly(L‐homoarginine) exhibited the remarkably enlarged CD spectrum of an extended conformation, while poly(L‐arginine) forms the α‐helix by interacting with the agent. Thus poly(L‐homoarginine), compared with poly(L‐arginine), has a much lower ability to form the α‐helical conformation by interacting with anions. The stronger hydrophobicity of homoarginine residue in comparison with

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190603

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

年代:1980

数据来源: WILEY

摘要:

AbstractCircular dichroism has been commonly employed to infer the conformation of DNA in solution. The basis of the conformational assignments is the work of Tunis‐Schneider and Maestre, wherein CD spectra of DNA were obtained under conditions comparable to those employed in the x‐ray diffraction studies of A‐, B‐, and C‐DNA. It has recently been suggested that the CD spectrum of DNA in chromatin, which is similar to the CD spectrum of the C‐form DNA, is a superposition of the normal B‐DNA spectrum and a single negative band, centered at 275 nm. This negative band is qualitatively identical to the spectrum for condensed Ψ‐form DNA. We have employed the hydrodynamic methods of quasielastic light scattering and sedimentation velocity to determine the extent of DNA tertiary structural alteration in 5.5MLiCl as a possible explanation of the C‐form CD spectrum. These studies suggest an eightfold contraction of the Stokes hydrodynamic volume for calf thymus DNA in going from 0.4MNH4Ac to 5.5MLiCl, with no change in molecular weight. The estimated maximum presistence length of DNA in 5.5MLiCl is estimated to be 20.0 nm compared to the “minimum” value of 44.7 nm in NaCl solutions. The value 20.0 nm corresponds to a maximum radius of 16.7 nm for a “continuously coiled” cylinder of DNA, which compares with the value 5.0 nm of DNA in the nu

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190604

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

年代:1980

数据来源: WILEY

摘要:

AbstractA new representation of protein structure is obtained by the angular coordinate transformations ηi= (ϕi+1−ψi)/2 and ξi= ϕi+1+ψiwith careful mathematical attention to the cyclical boundary conditions of all of the variables involved. From published ϕ‐ψ data it is possible to obtain a new η‐ξ plot. As the angle ξiis varied from – 180° through 0° to + 180° in this plot, the local helicity of the polypeptide chain changes continuously and contiguously without sudden reversals in handedness. The variable, ηi, gives the torsional position of theith peptide group. Some peptide groups in proteins, such as the second peptide residue in a type II β‐turn, are nonhydrogen‐bonded and can undergo considerable torsional oscillation. In such cases the η angle should be represented by a line whose length reflects the allowed dynamical variations in the peptide torsional position. Certain peptide residues in proteins may be able to undergo a complete torsional rotation of 360°. Such residues would be represented on the η‐ξ plot as a straight line across the plot parallel to the abscissa. Other examples of the possible usefu

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190605

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

年代:1980

数据来源: WILEY

摘要:

AbstractTertiary structure of globular proteins has traditionally been analyzed in terms of the organization of secondary structure elements. This paper presents a method for systematically identifying different topological features of the convolutions of the backbone. We define a loop as a segment of chain whose end residues are in contact. We find some loops which are threaded by another segment of chain passing through the loop or actually linked with another loop. Fifty‐six loop threadings were found among the 20 proteins studied, all of them occurring in a subset of seven proteins. In our sample, threadings and linkings were generally found if and only if the protein has more than 200 residues. To account for the existence of these topological features, despite their apparent entropic unfavorability, we have proposed a number of kinetic mechanisms by which they may form without a thread actually passing through a loop. We have found that almost all loop threadings possess structural features that would make one of these mechanisms plausibl

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190606

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

年代:1980

数据来源: WILEY

摘要:

AbstractThe concept of bends or chain reversals [nonhelical dipeptide sequences in which the distanceR3(i,i+3) between the Cαatoms of residuesiandi+3 is ≦ 7.0 Å] has been extended to define double bends as tripeptide sequences, not in an α‐helix, in which two successive distancesR3(i,i+3) andR3(i+1,i+4) are both ≦7.0 Å, with analogous definitions for higher‐order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher‐order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well‐defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution ofR3distances does not differ in single and multiple bends. However,R4(the distance between the Cαatoms of residuesiandi+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value ofR4in many multiple bends is near those for α‐helices. In some other multiple bends,R4is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cαatoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right‐handed (like an α‐helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single‐bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α‐helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual‐bond dihedral angles differ, have conformations that are very different from an α‐helix. They act as chain reversals occuring overthreeresidues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190607

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

年代:1980

数据来源: WILEY

摘要:

AbstractThe preferential orientations of the purine bases in dinucleoside monophosphates such as ApA, ApG, and GpA in 10−2Mneutral aqueous solutions have been investigated by proton relaxation at 250 MHz. These orientations are deduced from computer simulations of the magnetization recovery curves following a 180° nonselective pulse. The distances between the H(8) proton of a base and the ribose ring protons which are used in these calculations are obtained by minimization as a function of the glycosyl torsion angle ϒ of the standard deviation between the isotropic reorientation correlation times τRderived from the relaxation rates of these protons. The average H(1′) – H(8) distance obtained by this procedure may be readily verified from the reduction of the H(1′) relaxation rate when H(8) is substituted by a deuteron. The limits of validity of the assumption of a single correlation time τRgoverning the proton relaxation have been estimated, taking into account several possible internal motions, e.g., the rotation of the base, of the methylene exocyclic group and the N ⇄ S interconversion of the ribose ring. For 10−10<τR<2 × 10−10sec, it appears that the influence of these motions on the proton relaxation becomes perceptible when the jump rates among equilibrium positions exceed ca. 109sec−1.The whole of the experimental results show that for the ribose ring N conformer, the orientation of the bases is found in the ranges 60°<ϒ<80° (syn) and 180°<ϒ<210° (anti). For ribose S conformer, it is observed that this orientation is mainlysynwith 5°<ϒ<90°. The average H(1′) – H(8) distance provides semiquantitative information on the overallsynorantiorientations of the base in each nucleoside moiety. At 298 K the population of theanticonformer is found to increase in the order A‐pG

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190608

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

年代:1980

数据来源: WILEY

摘要:

AbstractDynamic light scattering experiments were performed on solutions of the bacteriophages T7 and T4B in order to obtain the rotational diffusion coefficients of these phages. Correlation functions were determined from the depolarized intensity scattered in the forward direction. The apparatus used in this study is described in detail. Particular attention is paid to the minimalization of the depolarized intensity due to double scattering. If double scattering cannot be neglected, the correlation function of the depolarized field is the sum of the correlation functions resulting from single and double scattering. It is shown that by correcting for double scattering, it is then possible to obtain the rotational diffusion coefficient of the macromolecules. Although the optical anisotropy of both T4B (retracted fibers) and T7 is very small, the experimental conditions could be chosen in such a way that no depolarized scattering due to double scattering was observed. The measured rotational diffusion coefficients for T4B and T7 areD R 20,w= 258 ± 12 and 4528 ± 100 sec−1, respectively. These values compare very well with those obtained by electric birefringence expe

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190609

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

年代:1980

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190610

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

年代:1980

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190601

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

年代:1980

数据来源: WILEY