摘要:

AbstractThe persistence length of lugworm cuticle collagen in 0.1Macetic acid was evaluated as 1600 ∼ 1800 Å by Yamakawa‐Fujii's model for a wormlike chain from the sedimentation constant and the intrinsic viscosity. The persistence length was further examined for a series of sample “collagen sonicates” produced by varying the duration of sonic irradiation. To estimate the salt effect on the persistence length, measurements were made over a range of NaCl concentrations from 0 to 0.1M. The results showed that the cuticle collagen and collagen sonicates had identical values of persistence length and that the neutral salt effect for the cuticle collagen was far smaller than that

ISSN:0006-3525    

DOI:10.1002/bip.360210402

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe pertinent correlation function for nmr dipolar relaxation of31P by its neighboring protons in DNA is derived for a comparatively realistic model of the internal Brownian motions. These motions include the collective torsional deformation modes of the elastic filament, uncoupled local overdamped reorienting motions of the P‐H vectors in harmonic potential wells within the nucleotide unit, and the compartively slow end‐over‐end rotations of thelocalhelix axis. These latter slow axial tumbling motions essentially completely determineT2but have virtually no effect onT1or the nuclear Overhauser effect (NOE), which are governed almost exclusively by rapid torsional deformations and local reorientations on the nanosecond time scale. The essential behavior of the relevant correlation function for the collective torsional motions has recently been determined experimentally in this laboratory using the decay of fluorescence polarization anisotropy of bound ethidium dye [J. C. Thomas et al. (1980)Biophys. Chem.12, 177–180]. By using that result to carry out nmr relaxation calculations for various amplitudes and time constants of the uncoupled local motions and comparing them with the experimental data, it can be demonstrated that (within this model of purelydipolarrelaxation), only rather small rms amplitudes of local reorientations (<7°) occur and that their relaxation times are near 1 ns. Contrary to previous conclusions in the literature, the collective torsional deformation modes actually make the dominant contribution toT1and NOE. Att= 1 ns the total rms azimuthal displacement of the P‐H vector in this model is 19.5°, which results from a superposition of torsional deformations with rms displacement 18.2° and uncoupled local motions with rms displacement 7°. The contribution of pure chemical shift anisotropy (CSA) to the 1/T1relaxation rate is calculated for the first time for the case when torsional deformation modes predominate, and it is predicted to be 46% of the corresponding dipolar relaxation rate or 31% of the total relaxation rate. Unusual magnetic field strength dependence of the pure CSA and dipolar contributions is predicted to arise as a consequence of the collective torsional deformation modes. This seriously weakens empirical arguments in favor of a small (<10%) CSA contribution. In any case, a detailed interpretation ofT1and NOE incorporating both dipolar and CSA relaxation must await the evaluation of the CSA:dipolar interference term, or crossterm, contribution to the relaxation rate. The contribution of pure CSA to 1/T2relaxation is likewise calculated for the case when local reorienting motions are negligible; it is found to be ≲16% of the corresponding dipolar relaxation rate for the comparatively short (300–600‐base‐pair) DNA fragments of interest. For high‐molecular‐weight DNAs we predict that the slow Rouse‐Zimm coil‐deformation modes will dominate 1/T2relaxation and the linewidth. Dynamic light‐scattering and other evidence is presented that the remarkable loss of nmr signal from DNA on addition of ethidium bromide, as reported by Hogan and Jardetzky, is actually a consequence of phase separation in such concentrated solutions. A pronounced decrease inT2, due to greatly hindered axial tumbling in the more concentrated phase, is advanced as a plausible line‐broadening explanation for the apparent loss of

ISSN:0006-3525    

DOI:10.1002/bip.360210403

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

年代:1982

数据来源: WILEY

摘要:

AbstractWe report on a computer experiment in which, using Monte Carlo techniques, we considered a three‐turn (30‐base‐pairs) B‐DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B‐DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B‐DNA strands are fully analyzed and described in detail. A model for base‐pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism

ISSN:0006-3525    

DOI:10.1002/bip.360210404

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

年代:1982

数据来源: WILEY

摘要:

AbstractAbsorption and circular dichroic (CD) spectra of the π‐π* transition near 200 nm are calculated for poly(Gly), poly(Ala), poly(Abu), and poly(Val) in the βP(paralle) and βA(antiparallel) pleated‐sheet structures using the dipole interaction model and including interactions among all atoms; optical parameters were obtained from previous studies of related molecules. Most of the calculations are for structures with one or three chains of six residues each. The oscillator strength and splitting of the π‐π* modes are found to be affected only to a small extent by variations in side‐chain structure and conformation, whereas the CD spectrum is very sensitive to these variations. Poly(Gly) and poly(Ala) β‐structures in uniform, planar lattices do not show sufficient rotational strength to account for observed CD spectra. Poly(Abu) and poly(Val) β‐structures in uniform, planar lattices show rotational strengths comparable to experiment when χ1is near −60° for βA‐structures or in a broad range near 140° for βP‐structures. Poly(Ala) in uniformly twisted βA‐ and βP‐structures or in irregular βA‐structures corresponding to regions of the crystal structure of concanavalin A also show enhanced rotational strengths in the principal π‐π* CD band. Absorption and CD spectra calculated for poly(Abu) in uniform βA‐ and βP‐structures are compared with experimental data on poly(Lys) in the β‐form, assuming side‐chain conformations in Abu that maximize the intensity of the principal CD band. The calculations for the βA‐form show the b

ISSN:0006-3525    

DOI:10.1002/bip.360210405

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

年代:1982

数据来源: WILEY

摘要:

AbstractWe have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to beD= 8.56 × 10−8cm2/s. For the tail, we foundD= 5.88 × 10−8cm2/s by QLS, andD= 6.02 × 10−8cm2/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex‐to‐vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320‐Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube‐sheath‐connector complex 1050‐Å long and 240 Å in diameter, the calculatedDis 5.93 × 10−8cm2/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the struc

ISSN:0006-3525    

DOI:10.1002/bip.360210406

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe complexes of the three BrCN‐cleaved fragments of sperm whale apomyoglobin with hemin were studied by circular dichroism (CD). In native myoglobin, the heme is located in the middle fragment; the isolated peptide (residues 56–131), however, produces little extrinsic Cotton effects by the addition of hemin, although about four molecules of hemin are bound to this peptide. In marked contrast, the COOH‐terminal peptide (residues 132–153), which binds three hemin molecules, shows strong Cotton effects in the Soret bands and drastically changes its conformation from unordered to highly helical. The Arg‐modified or Lys‐deaminated peptide no longer undergoes conformational changes by the addition of hemin, suggesting that the two propionic acid groups of one hemin molecule interact with the Arg residue and one of the Lys residues, which stabilizes the induced helical conformation. The NH2‐terminal peptide (residues 1–55) binds one hemin molecules, and the helicity of this fragment is slightly enhanced by the addition of hemin. Both the CD and difference absorption spectra indicate that the mode of interaction between the peptides and hemin are different for the three apomyog

ISSN:0006-3525    

DOI:10.1002/bip.360210407

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

年代:1982

数据来源: WILEY

摘要:

AbstractIf solution scattering curves can be accurately predicted from structural models, measurements can provide useful tests of predictions of secondary and tertiary structure. We have developed a computational technique for the prediction and interpretation of x‐ray scattering profiles of biomolecules in solution. The method employs a Monte Carlo procedure for the generation of length distribution functions and provides predictions to moderate resolution (∼5 Å). In addition to facilitating the assignment and interpretation of features in a solution scattering profile, the method also allows the elucidation of the role of protein motion in shaping the final scattering curve. The effect of protein motion on a scattering profile is investigated by generating scattering curves from several consecutive 0.147 ps atomic coordinate frames from a molecular dynamics simulation of the motion of bovine pancreatic trypsin inhibitor (BPTI) [McCammon, J. A.&Karplus, M. (1980)Annu. Rev. Phys. Chem.31, 29–45]. The theoretical approach is applied to chicken egg white lysozyme and BPTI, and the overall features in the resulting theoretical scattering profiles match well with the experimental solution scattering curves recorded on film. It is apparent from this study that the scattering profile prediction technique in conjunction with other experimental methods may have value in testing ideas of conformational change based on crystallographic studies; investigations of this type would include a comparison of predicted scattering curves generated from a variety of crystallographic models with an actual scattering profile of the biomolecule in so

ISSN:0006-3525    

DOI:10.1002/bip.360210408

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

年代:1982

数据来源: WILEY

摘要:

AbstractPoly(L‐lysine) of various molecular weights between 2700 and 475,000 was spin‐labeled. From the electron spin resonance spectra, the degree of freedom of the nitroxide was determined by calculation of the rotational correlation time as the poly(L‐lysine) underwent the pH‐induced random coil to α‐helix conformational transition. In general, the rotational correlation time of the nitroxide increased as the pH was increased, indicating a more restricted environment for the spin label when poly(L‐lysine) is deprotonated. For the high‐molecular‐weight poly(L‐lysine) this corresponds to the formation of the α‐helix and indicates that the side chain–side chain interaction and decreased segmental motion of the backbone (slightly) restricts the motion of the spin label. For the 2700‐molecular‐weight poly(L‐lysine), previously shown not to assume a helical conformation at high pH, the increase in the rotational correlation time of the spin label indicates that the side chain–side chain interaction takes place after deprotonation but without helix formation. This may indicate that helix formationper seis not needed to produce the observed effect even with the high‐molecular‐weight polymers. The rotational correlation time of the spin label at a particular pH did not depend on the molecular weight of the poly(L‐lysine) over the 200‐fold range of molecular weights. This indicates that the rotational correlation time reflects the rotational mobility of the spin label in a localized environment and not the rotationa

ISSN:0006-3525    

DOI:10.1002/bip.360210409

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

年代:1982

数据来源: WILEY

摘要:

AbstractCD study of four modified nucleosides, constituents of tRNA molecules, revealed that 2‐thio‐5‐methyluridine and 5‐methyluridine in aqueous solution, 0.1NHCl, and organic solvents essentially occur in ananti‐conformation. 5‐Methylcytidine also occurs in ananti‐conformation similar to cytidine in aqueous solution and organic solvents, while 2‐thiocytidine dihydrate appears to occur in ananti‐conformation. It is stressed that the CD data of thionucleosides might be applied to the successfully conformational analysis

ISSN:0006-3525    

DOI:10.1002/bip.360210410

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

年代:1982

数据来源: WILEY

摘要:

AbstractClassical potential functions (CPF) calculations on 3′‐mononucleotides, the building blocks of nucleic acids, predict a correlation between the sugar ring pucker and the torsion angle Φ′ around the C3′O3′ bond. In ribonucleotides, the value of Φ′ depends on the sugar pucker, viz. the C2′‐endosugar pucker is associated with Φ′ = 210° and 270°, while the C3′‐endosugar pucker favors only Φ′ = 210°. On the other hand, in deoxyribonucleotides, both sugar puckers show a preference for Φ′ = 180°. These theoretical predictions are fully corroborated by the results obtained from x‐ray and nmr stud

ISSN:0006-3525    

DOI:10.1002/bip.360210411

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

年代:1982

数据来源: WILEY