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1.
DNA curvature influences the internal motions of supercoiled DNA.   总被引:3,自引:1,他引:3       下载免费PDF全文
W Kremer  K Klenin  S Diekmann    J Langowski 《The EMBO journal》1993,12(11):4407-4412
We present evidence that short curved DNA segments can act as mediators for the ordering of large domains in superhelical DNA. Using a non-invasive solution method (dynamic light scattering), we investigated the effect of permanently curved inserts on the solution structure and on the internal motions of superhelical plasmid DNA. We find that the dynamics of superhelical DNA are strongly influenced by sequence- or protein-induced bending: in superhelical plasmids containing curved inserts the amplitude of the internal motion is lower than that of non-curved controls. Furthermore, the relative arrangement of curved sequences in the plasmids can influence the overall shape of the superhelical DNA. On linearized forms of the plasmids, these effects are not observed.  相似文献   

2.
B Fanconi  W L Peticolas 《Biopolymers》1971,10(11):2223-2229
Using valence force field constants and a highly simplified model of the α-helix consisting of only two masses per repeat unit we have been able to very nearly reproduce the low frequency phonon dispersion curves which we had obtained earlier with the use of a seven mass model and a Urey-Bradley force field. Since the frequencies obtained from this latter model agree well with the observed Raman frequencies it appears that the low frequency chain motions of polypeptide chains may be calculated from a very simple model involving the amino acid residues as essentially a single mass. Such techniques appear to offer the possibility of making normal mode calculations for the chain dynamics of polypeptide chains of low symmetry such as proteins.  相似文献   

3.
Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid DNA, indicating that internal motions and/or dye wobbling contribute to the depolarization. The data are consistent with a model where the DNA fragments are considered to be rigid against bending but torsionally flexible, and where the dye can wobble within the intercalated site. We also discuss the possibility of correlated out-of-plane motions of the dye and the DNA bases.  相似文献   

4.
To describe low-frequency dynamics of DNA macromolecules a model is developed taking into account the hydrogen bond stretching in base pairs, the backbone flexibility and intranucleoside mobility. For double-stranded DNA the normal vibrations are found and the structure of low-frequency spectrum is determined. The agreement between theory and Raman spectroscopy data for B-DNA is demonstrated. Conformational dependences of vibration spectrum during the B----A and helix----coil DNA transitions are studied. The contribution coming from low-frequency mobility to the nucleic-protein recognition processes is discussed.  相似文献   

5.
6.
T Fujiwara  H Shindo 《Biochemistry》1985,24(4):896-902
31P nuclear magnetic resonances (NMR) of salmon sperm DNA, poly(rA).poly(rU), and poly(rA).poly(dT) fibers were measured as a function of relative humidity. The results indicated that the spectra were strongly perturbed by the molecular motions occurring in the hydrated fibers. The humidity dependence of the spectra at a number of orientations of the fibers relative to the magnetic field was reasonably explained by taking into account at least three motional modes, namely, conformational fluctuations, restricted rotation about a tilted axis, and rotational diffusion about the helical axis. The rotational diffusion about the helical axis was found to perturb the spectral line shapes most strongly, and its constants were 1.5 X 10(4) and 5.0 X 10(4) S-1 for DNA fibers at 92% and 98% relative humidities, respectively. A DNA-RNA hybrid, poly(rA).poly(dT), has been shown to adopt different conformations on two strands at high relative humidity [Zimmerman, S. B., & Pheiffer, B. H. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 78-82], which was unquestionably confirmed in the present study: that is, the 31P NMR spectra from the hydrated form of this polymer were clearly explained by assuming that one strand had an A-like conformation and the other a B-like conformation.  相似文献   

7.
A novel method for analysing molecular dynamics trajectories has been developed, which filters out high frequencies using digital signal processing techniques and facilitates focusing on the low-frequency collective motions of proteins. These motions involve low energy slow motions, which lead to important biological phenomena such as domain closure and allosteric effects in enzymes. The filtering method treats each of the atomic trajectories obtained from the molecular dynamics simulation as a "signal". The trajectories of each of the atoms in the system (or any subset of interest) are Fourier transformed to the frequency domain, a filtering function is applied and then an inverse transformation back to the time domain yields the filtered trajectory. The filtering method has been used to study the dynamics of the enzyme phospholipase A2. In the filtered trajectory, all the high frequency bond and valence angle vibrations were eliminated, leaving only low-frequency motion, mainly fluctuations in torsions and conformational transitions. Analysis of this trajectory revealed interesting motions of the protein, including concerted movements of helices, and changes in shape of the active site cavity. Unlike normal mode analysis, which has been used to study the motion of proteins, this method does not require converged minimizations or diagonalization of a matrix of second derivatives. In addition, anharmonicity, multiple minima and conformational transitions are treated explicitly. Thus, the filtering method avoids most of the approximations implicit in other investigations of the dynamic behaviour of large systems.  相似文献   

8.
9.
DNA polymerase (pol) beta is a two-domain DNA repair enzyme that undergoes structural transitions upon binding substrates. Crystallographic structures indicate that these transitions include movement of the amino-terminal 8-kDa lyase domain relative to the 31-kDa polymerase domain. Additionally, a polymerase subdomain moves toward the nucleotide-binding pocket after nucleotide binding, resulting in critical contacts between alpha-helix N and the nascent base pair. Kinetic and structural characterization of pol beta has suggested that these conformational changes participate in stabilizing the ternary enzyme-substrate complex facilitating chemistry. To probe the microenvironment and dynamics of both the lyase domain and alpha-helix N in the polymerase domain, the single native tryptophan (Trp-325) of wild-type enzyme was replaced with alanine, and tryptophan was strategically substituted for residues in the lyase domain (F25W/W325A) or near the end of alpha-helix N (L287W/W325A). Influences of substrate on the fluorescence anisotropy decay of these single tryptophan forms of pol beta were determined. The results revealed that the segmental motion of alpha-helix N was rapid ( approximately 1 ns) and far more rapid than the step that limits chemistry. Binding of Mg(2+) and/or gapped DNA did not cause a noticeable change in the rotational correlation time or angular amplitude of tryptophan in alpha-helix N. More important, binding of a correct nucleotide significantly limited the angular range of the nanosecond motion within alpha-helix N. In contrast, the segmental motion of the 8-kDa domain was "frozen" upon DNA binding alone, and this restriction did not increase further upon nucleotide binding. The dynamics of alpha-helix N are discussed from the perspective of the "open" to "closed" conformational change of pol beta deduced from crystallography, and the results are more generally discussed in the context of reaction cycle-regulated flexibility for proteins acting as molecular motors.  相似文献   

10.
We have conducted a polarized fluorescence photobleaching recovery (FPR) study of the rotational dynamics of ethidium azide labeled DNA. Polarized photobleaching experiments provide data on microsecond and millisecond molecular reorientation that complement the information available from nanosecond fluorescence depolarization studies. In polarized FPR experiments an anisotropic angular concentration of fluorophore is created by bleaching dye molecules in a preferred orientation with a short, intense pulse of polarized light. The sample is then weakly illuminated, and the temporal variation in the emitted fluorescence is monitored. The fluorescence signal will systematically change as molecules undergo post-bleach reorientation and the angular distribution of dye tends toward isotropy. We have observed that the time dependence of our microsecond FPR curves is also determined in part by nonrotational phenomena. To isolate the reorientational recovery we conduct our FPR experiments in two modes (called parallel and perpendicular) that differ only in the polarization of the bleaching light. A quotient function, R(t), is constructed from the data obtained in these two modes; the variation with time of this new quantity is governed solely by processes that are sensitive to the polarization of the incident light (e.g., molecular rotation). It is found experimentally that R(t) remains constant, as expected, for rotationally restricted DNA systems despite a temporal recovery in the parallel and perpendicular FPR curves. We also follow the dynamics of solutions of phage lambda DNA as revealed in the temporal dependence of R(t). This DNA system rotationally relaxes after approximately 100 microseconds and the dye/DNA complex reorients substantially during the 10-microseconds bleach period. Our FPR data are interpreted in terms of dynamic models of DNA motion.  相似文献   

11.
Structural models for non-helical DNA.   总被引:3,自引:0,他引:3       下载免费PDF全文
Structural modelling techniques are employed to explore the energetic requirements for the transformation of classical B DNA into unwound yet double-stranded DNA structures. Structural idealization using CORELS computer program of Sussman et al. followed by energy minimization using the EREF program of Levitt, leads to two regular non-helical models. In both models, the bases are conventionally paired and stacked, yet there is no net rotation between successive base pairs. One model, N1, has a 1-bp repeating unit; the second, N2, has a 2-bp repeating unit. The dihedral angles of the backbone all have values found either in the B or the Z form of DNA, except for the P-O5'-C5'-C4' angle, which is in the unprecedented g+ or g- domains. The energy difference found between the two N form models and B form DNA are 6.6 and 3.4 kcal/mol/nucleotide for N1 and N2 respectively. These relatively low energy differences encourage the idea that non-helical forms of DNA may contribute to the alternate DNA structures found in S1 nuclease sensitive and other regulatory regions of active genes.  相似文献   

12.
The dynamics of the Peyrard-Bishop model for vibrational motion of DNA dynamics, which has been extended by taking into account the rotational motion for the nucleotides (Silva et al., J. Biol. Phys. 34, 511–519, 2018) is studied. We report on the presence of the modulational instability (MI) of a plane wave for charge migration in DNA and the generation of soliton-like excitations in DNA nucleotides. We show that the original differential-difference equation for the DNA dynamics can be reduced in the continuum approximation to a set of three coupled nonlinear equations. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Numerical simulations show the validity of the analytical approach with the generation of wave packets provided that the wave numbers fall in the instability domain.  相似文献   

13.
High-resolution proton nuclear magnetic resonance (1H NMR) measurements were made on myosin, heavy meromyosin (HMM), myosin subfragment 1 (S1), light meromyosin (LMM), and actin. A strong signal from amino acid side chains undergoing motions too fast to be accounted for by simple rotations of groups on a rigid backbone was obtained from myosin. Comparison of myosin, HMM, S1, and LMM showed that the mobile region is located almost entirely in S1 and accounts for approximately 22% of its structure. Adenosine triphosphate (ATP) and ATP analogues had no measurable effect on the S1 spectrum. Actin, on the other hand, quenched the internal motions of S1. When S1 was titrated with actin, an association was obtained which was in agreement with other measured values. The actin effect was reversed by adding magnesium pyrophosphate (MgPPi) or adenyl-5'-yl imidophosphate (MgAMPPNP). Quantitative treatment of the broad signals from myosin and its subfragments substantiated the existence of two flexible regions in myosin. The highly mobile portion of myosin may be located in the "swivel" between S1 and the rest of myosin or in the actin binding site or in both. These possibilites are discussed, and a new possible mechanism for muscle cross bridge elasticity is proposed.  相似文献   

14.
15.
DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.  相似文献   

16.
DNA motions in the nucleosome core particle: a reanalysis   总被引:3,自引:0,他引:3  
J M Schurr  R L Schurr 《Biopolymers》1985,24(10):1931-1940
  相似文献   

17.
NMR structures of biomolecules are primarily based on nuclear Overhauser effects (NOEs) between protons. For the interpretation of NOEs in terms of distances, usually the assumption of a single rotational correlation time corresponding to a rigid molecule approximation is made. Here we investigate the effect of fast internal motions of the interproton vectors in the context of the relaxation matrix approach for structure determination of biomolecules. From molecular dynamics simulations generalized order parameters were calculated for the DNA octamer d(GCGTTCGC).d(CGCAACGC), and these were used in the calculation of NOE intensities. The magnitudes of the order parameters showed some variation for the different types of interproton vectors. The lowest values were observed for the interresidue base H6/H8-H2" proton vectors (S2 = 0.60), while the cytosine H5-H6 interproton vectors were among the most motionally restricted (S2 = 0.92). Inclusion of the motion of the interproton vectors resulted in a much better agreement between theoretically calculated NOE spectra and the experimental spectra measured by 2D NOE spectroscopy. The interproton distances changed only slightly, with a maximum of 10%; nevertheless, the changes were significant and resulted in constraints that were better satisfied. The structure of the DNA octamer was determined by using restrained molecular dynamics simulations with H2O as a solvent, with and without the inclusion of local internal motions. Starting from A- or B-DNA, the structures showed a high local convergence (0.86 A), while the global convergence for the octamer was ca. 2.6 A.  相似文献   

18.
Human lymphocytes have been used by several researchers to investigate the biological effect of electromagnetic fields (EMF). EMF modulate the response by lymphocytes to lectin stimulation. The size and direction of the effect depends both on the lymphocyte physiology and on the physical parameters characterizing the EMF. Lymphocytes have also been used to investigate the genotoxicity of EMF exposure.  相似文献   

19.
DNA polymerases maintain genomic integrity by copying DNA with high fidelity. A conformational change important for fidelity is the motion of the polymerase fingers subdomain from an open to a closed conformation upon binding of a complementary nucleotide. We previously employed intra-protein single-molecule FRET on diffusing molecules to observe fingers conformations in polymerase–DNA complexes. Here, we used the same FRET ruler on surface-immobilized complexes to observe fingers-opening and closing of individual polymerase molecules in real time. Our results revealed the presence of intrinsic dynamics in the binary complex, characterized by slow fingers-closing and fast fingers-opening. When binary complexes were incubated with increasing concentrations of complementary nucleotide, the fingers-closing rate increased, strongly supporting an induced-fit model for nucleotide recognition. Meanwhile, the opening rate in ternary complexes with complementary nucleotide was 6 s−1, much slower than either fingers closing or the rate-limiting step in the forward direction; this rate balance ensures that, after nucleotide binding and fingers-closing, nucleotide incorporation is overwhelmingly likely to occur. Our results for ternary complexes with a non-complementary dNTP confirmed the presence of a state corresponding to partially closed fingers and suggested a radically different rate balance regarding fingers transitions, which allows polymerase to achieve high fidelity.  相似文献   

20.
I Klapper  H Qian 《Biophysical journal》1998,74(5):2504-2514
We present a comparison of the continuous versus discrete models of large-scale DNA conformation, focusing on issues of relevance to molecular dynamics. Starting from conventional expressions for elastic potential energy, we derive elastic dynamic equations in terms of Cartesian coordinates of the helical axis curve, together with a twist function representing the helical or excess twist. It is noted that the conventional potential energies for the two models are not consistent. In addition, we derive expressions for random Brownian forcing for the nonlinear elastic dynamics and discuss the nature of such forces in a continuous system.  相似文献   

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