摘要:

AbstractRapidly relaxing components in the decay of the transient electric dichroism of DNA restriction fragments were reported by Diekmann et al. [(1982)Biophys. Chem.15, 263–270] and Pörschke et al. [(1987)Biopolymers26, 1971–1974]. These are analyzed using a new normal mode theory for weakly bending rods and assigned to bending. The longest bending relaxation times for fragments with 95–250 base pairs coincide with the theoretical curve calculated for a dynamic bending rigidity corresponding to a dynamic persistence lengthPd= 2100 Å. Analysis of the relative amplitudes of fast and slow components following weak orienting pulses is also consistent with a rather large dynamic persistence length. The enhancement of the relative amplitude of the fast component in large electric fields is attributed to steady‐state bending of initially perpendicular DNAs by the field. Several reasons are proposed why the dynamic bending rigidity is 4 times larger than the apparent static bending rigidity inferred from equilibrium persistence length measurements on the same

ISSN:0006-3525    

DOI:10.1002/bip.360300302

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

年代:1990

数据来源: WILEY

摘要:

AbstractWe have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x‐ray crystallographic structure [D. van der Helm et al. (1980)J. Am. Chem. Soc.102, 4224–4231]. The Al3+and Ga3+diamagnetic analogues, alumichrome and gallichrome, dissolved in d6‐dimethylsulfoxide (d6‐DMSO), were investigated via one‐ and two‐dimensional1H‐nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984)Bull. Math. Biol.46, 673–691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983)J. Comp. Chem.4, 187–217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the14N‐1H dipolar interaction, demonstrate that the x‐ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6‐DMSO at 23°C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CHαmultiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH‐CHαand NH‐NH Overhauser connectivities, which reflects the 〈r−6〉 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the “true” structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straightforward approach can be misleading since the nmr parameters are averaged over subs

ISSN:0006-3525    

DOI:10.1002/bip.360300303

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe three‐dimensional structures of ribonuclease (RNase) T1complexes with the inhibitors 2′‐guanylic acid (2′‐GMP), 3′‐guanylic acid (3′‐GMP), and 5′‐guanylic acid (5′‐GMP) were predicted by energy minimization studies. It is shown that these inhibitors can bind to RNase T1in either of the ribose puckered conformations (C2′‐endoand C3′‐endo) in solid state and exist in significant amounts in both forms in solution. These studies are in agreement with the x‐ray crystallographic studies of the 2′‐GMP–Lys25–RNase T1complex, where the inhibitor binds in C2′‐endopuckered conformation. These results are also in good agreement with the available1H‐nmr results of Inagaki et al. [(1985)Biochemistry24, 1013–1020], but differ from their conclusions where the authors favor only the C3′‐endoribose conformation for all the three inhibitors. The calculations explain the apparent discrepancies in the conclusions drawn by x‐ray crystallographic and spectroscopic studies. An extensive hydrogen‐bonding scheme was predicted in all the three complexes. The hydrogen‐bonding scheme predicted for the 2′‐GMP (C2′‐endo)–RNase T1complex agrees well with those reported from x‐ray crystallographic studies. In all three complexes the base and the phosphate bind in nearly identical sites independent of the position of the phosphate or the ribose pucker. The glycosyl torsion angle favors a value in the +synrange in the 2′‐GMP(C2′‐endo)–RNase T1, 3′‐GMP(C2′‐endo)–RNase T1, and 3′‐GMP(C3′‐endo)–RNase T1complexes; in the high‐synrange in the 2′‐GMP(C3′‐endo)–RNase T1complex; and in the ‐synrange in the 5′‐GMP(C2′‐endo)–RNase T1, and 5′‐GMP(C3′‐endo)–RNase T1complexes. These results are in agreement with experimental studies showing that the inhibitory po

ISSN:0006-3525    

DOI:10.1002/bip.360300304

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

年代:1990

数据来源: WILEY

摘要:

AbstractTeichoic acid (TA) isolated from the gram‐positive bacteriaS. aureusbinds cationic dyes like pinacyanol (PCYN), 1,9‐dimethyl methylene blue, acridine orange, etc., depicting blue‐shifted metachromasia, and they bind the cationic dye carbocyanine depicting the red‐shiftedJband. TAs do not show any uv absorption band, and exhibition of tailing CD in the short uv region hints at its chiral conformation. Chiral conformation of TA has been confirmed from the induction of strong biphasic CD in the TA–carbocyanine system.Relative affinities for Ca2+, Mg2+, and Na+have been probed from the disruption of metachromasia of the TA–dye system by these ions. Results show Ca2+and Mg2+to be almost equally effective in destroying the metachromasia of the TA–PCYN system, thus not supporting the hypothesis of special affinit

ISSN:0006-3525    

DOI:10.1002/bip.360300305

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe Young's dynamical modulus(E)and the DNA film logarithmic decrement (v) at frequencies from 50 Hz to 20 kHz are measured. These values are investigated as functions of the degree of hydration and temperature. Isotherms of DNA film hydration at 25°C are measured. The process of film hydration changing with temperature is studied. It is shown that the Young's modulus for wet DNA films (E= 0.02–0.025 GN m−2) strongly increases with decreasing hydration and makesE= 0.5–0.7 GN m−2. Dependence ofEon hydration is of a complex character. Young's modulus of denatured DNA films is larger than that of native ones. All peculiarities of changing ofEandvof native DNA films (observed at variation of hydration) vanish in the case of denatured ones. The native and denatured DNA films isotherms are different and depend on the technique of denaturation. The Young's modulus of DNA films containing>1 g H2O/g dry DNA is found to decrease with increasing temperature, undergoing a number of step‐like changes accompanied by changes in the film hydration. At low water content (<0.3 g H2O/g dry DNA), changing ofEwith increasing temperature takes place smoothly. The denaturation temperature is a function of the wat

ISSN:0006-3525    

DOI:10.1002/bip.360300306

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe proline residues in proteins are known to play an important structural role. Recently, the role of a proline residue in the middle of right‐handed α‐helical segments of peptides has been the focus of attention. This role seems to be particularly important in the case of membrane proteins and in the tight packing of globular proteins. In the present study the right‐handed α‐helical region of the Ala‐Pro dipeptide and of polypeptides containing this group have been investigated. Crystal structures of proline‐containing α‐helices from some proteins have been analyzed and energy minimization studies on some model fragments containing Ala‐Pro in the right‐handed α‐helical conformation have been carried out using flexible geometry. The present calculations indicate that the right‐handed α‐helical region of conformational space is an energetically favored region that can also accommodate Ala‐Pro in longer segments of right‐handed α‐helix. This is achieved due to minor variations in some of the internal parameters. Deviations in the backbone parameters of proline in the right‐handed α‐helix lead to a kink of about 23° in the helix axis. These deviations have been characterized and a set of standard values has been suggested for producing such a kink. These values can be used for model building and as starting points for further minimization studies. Previous energy minimization studies have been done using rigid geometry. This may explain why the minimum for Ala‐Pro in the right‐handed α

ISSN:0006-3525    

DOI:10.1002/bip.360300307

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe hydrodynamics of the bacterial elongation factor EF‐Tu have been studied in the presence of its ligand guanosine‐5′‐diphosphate (GDP) by sedimentation in the ultracentrifuge and quasielastic light scattering. Sedimentation studies have made it possible to establish experimental conditions under which only negligible aggregation of the protein occurs (neutral pH, concentration<3 mg/mL). Analysis of the light intensity autocorrelation functions under these conditions revealed two independent scattering species with diffusion coefficients of 0.71 × 10−6and 0.04 × 10−6cm2s−1. The material with the lower diffusion coefficient, i.e., the aggregates, represented less than 1% of the total number of EF‐Tu particles. The other 99% diffused as monomeric molecules with a molar mass corresponding to the value calculated from the known primary structure of the protein. The hydrodynamic parameters derived from the experimental data suggest that EF‐Tu·GDP in solution is close to

ISSN:0006-3525    

DOI:10.1002/bip.360300308

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe effect of gel pore size on the anomalous mobility of certain curved DNA restriction fragments in polyacrylamide gels was studied by comparing the electrophoretic mobilities of normal and anomalous fragments in gels of varying composition but constant acrylamide concentration. Molecular weight ladders were prepared from two 147 base pair G‐C rich restriction fragments, called 12A (anomalous) and 12B (normal), obtained from the MspI digestion of plasmid pBR322. The electrophoretic mobilities of multimers of the two fragments increasingly diverged with increasing molecular weight. The anomalous mobility of fragment 12A was essentially independent of gel pore size, regardless of whether the pore size was varied by increasing the acrylamide concentration at constant cross‐linker concentration or by increasing the cross‐linker concentration at constant acrylamide concentration. The anomalous mobility of higher multimers of fragment 12A decreased with increasing gel pore size when the pore size was varied by changing the gel concentration. However, when the gel pore size was changed by varying the cross‐linker concentration at constant acrylamide concentration, the anomalous mobility of higher multimers of fragment 12A went through a maximum and then decreased as the pore size was increased. Copolymerizing acrylamide with high molecular weight linear polyacrylamides had no effect on the anomalous mobility of the 12A multimer ladder, even though the apparent absolute mobilities of all fragments increased markedly. Only by incorporating charged residues into the gel matrix or by copolymerizing acrylamide with the intercalator ethidium bromide could the difference in mobility between the 12A and 12B multimer ladders be substantially reduced or eliminated. Similar results were observed with a molecular weight ladder containing 78 base pair repeats of the bending locus of kinetoplast DNA. These results suggest that pore size alone is not responsible for the anomalously slow migration of curved DNA molecules in polyacrylami

ISSN:0006-3525    

DOI:10.1002/bip.360300309

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe interaction of Ca2+ions in 10 mMNaCl at 17°C with polynucleotides of different primary and secondary structure has been investigated. The experimental results show the following:1The affinity for calcium ion depends on the secondary structure of the polynucleotide and not, within the experimental error, on the base sequence.2The following hierarchy in calcium ion binding can be established: A‐RNAs>B‐DNAs>single‐stranded RNAs. The polyG binding curve is analogous to that of A‐RNAs; this strongly suggests that it does not adopt a single‐stranded structure in our experimental conditions.3Apart from the case of single‐stranded RNAs, where both Manning's and Poisson–Boltzmann models seem to fit the data well, the Poisson–Boltzmann equation reproduces the experimental points better than the Manning's theory, which overestimates the affinity of the double‐stranded nucleic aci

ISSN:0006-3525    

DOI:10.1002/bip.360300310

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

年代:1990

数据来源: WILEY

摘要:

AbstractA straightforward hierarchical statistical–mechanical approach is shown to enable one to describe the stability of the alpha helix in the presence of side‐chain interactions. The formulation can be used with even the simple nearest‐neighbor models and it is demonstrated explicitly with the popular 2 × 2 Zimm‐Bragg model [B. H. Zimm and J. K. Bragg (1959)J. Chem. Physics31, 526–535]. It involves a conceptual dissection of the polypeptide chain into interacting blocks; the behavior of any block with side‐chain interactions is treated then with conventional binding polynomial techniques. This dissection is a manifestation of “nesting,” which is a hierarchical framework for the description of the behavior of complex macromoecules [C. H. Robert, H. Decker, B. Richey, S. J. Gill, and J. Wyman (1987)Proc. Natl. Acad. Sci.84, 1891–1895]. The method is demonstrated through applications to existing detailed data for the pH and salt dependences of the helix–coil transition in the S peptide and i

ISSN:0006-3525    

DOI:10.1002/bip.360300311

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

年代:1990

数据来源: WILEY