摘要:

AbstractMolecular and harmonic dynamics simulations have been performed for a decaglycine α‐helix. The extent of anharmonicity for various observables is studied by a direct comparison of the two types of simulations, at temperatures ranging from 5 to 300 K. The fluctuations of the cartesian, internal and normal mode coordinates, and their time dependence, are analyzed. The heat capacity of the α‐helix is evaluated both from the temperature response of the system to an energy perturbation and from the fluctuations in the temperature of the system. It is shown that the anharmonicity depends on the kind of observable. The root mean square atomic fluctuations have significant anharmonic components at temperatures above 100 K. In contrast, the dihedral angle fluctuations are much closer to being harmonic at all the temperatures considered. The analysis of potentials of mean force experienced by individual atoms shows that atomic displacements have approximately Gaussian distributions from 50 to 300 K, with different force constants at each temperature (quasi‐harmonic model). At 300 K, the force constants obtained by molecular dynamics are significantly lower than in the harmonic case. The time dependence of the projection of the molecular dynamics displacements on the normal mode coordinates shows that mode mixing is important above 100 K. The motions of the helix associated with the low‐frequency normal modes are described and il

ISSN:0006-3525    

DOI:10.1002/bip.360290402

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe program FANTOM (fast Newton–Raphson torsion angle energy minimizer) performs minimizations of the ECEPP/2 energy function for proteins with the Newton–Raphson method. It is implemented for use with conventional computer hardware. The torsion angles are chosen as independent variables. The first and second derivatives are calculated with a previously described rapid algorithm. For the matrix inversion a modified Cholesky factorization is used. A line search adjusts the step length and nonbonded interactions can be calculated with a cutoff. The following tests of the program are described: All local minima of the ECEPP/2 energy function for the amino acids glycine and alanine were determined. An exhaustive search by more than 16,000 independent energy minimizations was used to identify low‐energy structures of Met‐enkephalin, which were then compared with previously published structures of this pentapeptide. To investigate the use of FANTOM with disulfide bonds, it was applied with conotoxin. As an illustration of the intended primary use of the program, an energy refinement of the structure of the basic pancreatic trypsin inhibitor determined by nmr spectroscopy in solution is de

ISSN:0006-3525    

DOI:10.1002/bip.360290403

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe solution structure of an α‐amylase inhibitor, tendamistat, calculated from nmr data with the distance geometry program DISMAN is subjected to restrained energy minimization. To study the influence of force field parametrizations and the convergence behavior of refinement algorithms, two different programs were used. AMBER is an established software package including a steepest descent and/or conjugent gradient optimizer in the Euclidian space; the name AMBER also represents a force field. The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) is a new restrained energy refinement implementation of the Newton–Raphson algorithm, which uses second derivatives of the conformational energy in dihedral angle space with the ECEPP/2 force field. For both programs the normal energy force field was supplemented with an additional potential of the form ΣA(di−ui)6(ifdi>ui), which enforces upper limitsuito selected distancesdias measured by nmr. Improvements of the intramolecular interactions with a decrease of the internal energies of about 1000 kcal/mol could be achieved without increasing the distance constraint violations. The restrained energy refinements caused only small changes of the molecular geometries: The root mean square distance values for the backbone atoms between the initial DISMAN structure and the refined structures are about 0.5 Å for AMBER and about 0.7 Å for FANTOM. Local conformational changes during the restrained energy minimizations are analyzed with respect to hydrogen‐bond formation, and with respect to comparisons of the solution structure and the crys

ISSN:0006-3525    

DOI:10.1002/bip.360290404

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

年代:1990

数据来源: WILEY

摘要:

AbstractResonance Raman spectra have been obtained at several uv wavelengths (200–266 nm) for poly(rA)‐poly(rU), poly(dA‐dU), poly(dA)‐poly(dT), and poly(dA‐dT), representing nucleic acid duplexes containing A‐U and A‐T base pairs with different stacking interactions and different backbone conformations. Frequency shifts are seen in the exocyclic modes corresponding to coupled C4O and C5C6 stretching of U and T, although the NH2scissors frequency of A is unshifted relative to that of the mononucleotide. These frequency patterns are interpreted as the superposition of H bonding and dipole–dipole coupling effects. Strong hypochromism is seen for most of the ring modes, resulting from the absorption hypochromism and from shifts in the electronic transitions due to stacking. The effects are larger for A bands in the homopolymers than in the heteropolymer duplexes, reflecting the larger influence of A/A than A/U(T) stacking. Poly(rA)‐poly(rU) stands out among these polymers in showing 10 cm−1downshifts in one U and several A modes. These shifts may be related to the A form structural parameters of this duplex, but the physical m

ISSN:0006-3525    

DOI:10.1002/bip.360290405

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

年代:1990

数据来源: WILEY

摘要:

AbstractWe present the results of free energy perturbation/molecular dynamics studies on B‐DNA · daunomycin and B‐DNA · 9‐aminoacridine complexes as well as on B‐DNA itself in order to calculate the free energy differences between complexes having different base pair sequences. The results generally reproduce the trends observed experimentally, i.e., preferences of acridine and daunomycin to bind to a specific base sequence in the DNA. This is encouraging, given the simplicity of the molecular mechanical/dynamical model in which solvent is not explicitly

ISSN:0006-3525    

DOI:10.1002/bip.360290406

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

年代:1990

数据来源: WILEY

摘要:

AbstractWe have investigated the effects of changes in solution composition on the mechanical properties of rings of arterial elastin. The time course of force equilibration at constant strain following a change in the composition of the bathing solution was measured. Both the force developed during slow extension and force relaxation following rapid straining were also measured in each of the test solutions. The results are difficult to summarize because all of the primitive quantities measured—sample dimension, slope of the force‐extension curve, force overshoot and time of relaxation—as well as the derived quantities such as elastic modulus changed in different and apparently uncorrelated ways. Changes in pH and ionic composition of the bathing solution had small effects consistent with the low fixed charge density of elastin. Solutions of glucose, sucrose, and ethylene glycol had larger effects consistent with changes in hydrophobic interactions. The viscosity of the solution that penetrated the intrafibrillar space of the elastin appeared to be a major determinant of the dynamic res

ISSN:0006-3525    

DOI:10.1002/bip.360290407

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe pulsed‐field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical predictions as well as to find optimum conditions for effecient separation of large DNA fragments. In the present study, deformation of large DNA fragments (40 ∼ 70 kilobase pairs) imbedded in agarose gels were investigated by using the transient electric birefringence (TEB) technique under both singular polarity and bipolarity electric pulses at low applied electric field strengths (E≤ 5 V/cm). The steady‐state optical retardation (δs) of DNA molecules is linearly proportional toE2. At a givenE, the amplitude of optical retardation [δ(t)] increases monotonically with the pulse width (PW) and then reaches a plateau value [δ(t= 0) = δs] wheret= 0 denotes the time when the applied field is turned off or reversed. The field‐free decay time (τ ∼ a few minutes) is several orders of magnitudes slower than that from previous TEB observations using high electric field strengths (E∼ kV/cm) and short pulse widths (PW∼ ms). The degree of deformation (stretching and orientation) and the time of restoration to the equilibrium conformation of overall DNA chains have been related to δ and τ. In field inversion measurements, exponentially rising and linearly falling of birefringence signals in the presence of forward/inverse applied fields were observed. The rising and falling of birefringence signals were reproducible under a sequence of alternating pulses. Comparison of our results with literature findings and discussions with

ISSN:0006-3525    

DOI:10.1002/bip.360290408

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

年代:1990

数据来源: WILEY

摘要:

AbstractChitosan can be converted into a polycation by dissolving it in an acid, and this polycation (I) induces blue‐shifted metachromasia in suitable anionic dyes, C.I. acid red 88 and C.I. acid orange 7, after reacting with the dyes with 1 : 1 stoichiometry (P/D). Both these dye–polymer systems exhibit strong biphasic CD in the visible range. Biphasic CD, as well as blue‐shifted metachromasia, indicates strong dye–dye interactions in these systems. Monophasic CD are observed only in conditions where metachromasia is partially disrupted due to poor dye–dye interactions.The 21‐helical conformation, as confirmed for the present polymer chitin as well as for neutral chitosan, seems to be inadequate in explaining the observed resul

ISSN:0006-3525    

DOI:10.1002/bip.360290409

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe interaction of mono‐ and divalent metal ions with the nucleic acid base pairs A:T and G:C has been studied using ab initio self‐consistent field Hartree–Fock computations with minimal basis sets. Energy‐optimized structures of the two base pairs with a final base–base distance ofL= 10.35 Å have been determined and were further used in calculations on ternary complexes Mn+– A:B together with previously computed coordination geometries of the cations at adenine (Ade), thymine (Thy), and guanine (Gua). Besides the binding energy of the various metal ions to the base pairs, changes in the stability of the H bonds between Ade and Thy or Gua and Cyt have been determined. Polarization effects of the metal ion on the ligand turned out to increase the binding between complementary bases. Regardless of the metal species, cation binding to Gua N(3) and Thy O(2) leads to a special increase in H‐bond stability, whereas binding to Ade N(3) changes the H‐bond stability least. Situated in between are the stabilizing effects caused by Gua and Ade N(7) coordination. A remarkable relation between the stability of the H bond and the distance from metal binding site to H bonds was found. This relationship has been rationalized in terms of partial charges of the atoms participating in H bonding, which can reveal the trend in the electrostatic part of total H bond energy. It can be shown that a short distance between coordination site and acceptor hydrogen increases the H‐bond strength substantially, while a long distance shows minor effects as supposed. On the other hand, the opposite effect is observed for the influence of the distance between binding site and donor atom. A comparison of our findings with a new model of transition metal ion facilitated rewinding of denatured DNA proposed by S. Miller, D. VanDerveer, and L. Marzilli is given [(1985)J. Am. Chem. S

ISSN:0006-3525    

DOI:10.1002/bip.360290410

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

年代:1990

数据来源: WILEY

摘要:

AbstractMonte Carlo computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water–water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar–phosphate backbone were examined, and the probabilities of occurrence for one‐ and two‐water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x‐ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and ammonium salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation to compete unfavorably with the adjacent donor site at guanine N2. There is, however, a significant probability of finding a one‐water G‐N3–W–G‐N2 bridge indicated in the simulation. An explanation for the guanine N3 discrepancy in terms of electrostatic potentials is also offered. The calculated one‐and two‐water bridges in the rGpC hydration complex coincide in a number of cases to those observed in the ordered water structure of the sodi

ISSN:0006-3525    

DOI:10.1002/bip.360290411

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

年代:1990

数据来源: WILEY