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  • Polymer and Materials Science  (21)
  • conformational transitions  (1)
  • molecular dynamics  (1)
  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH3+ prototype test probe with B-form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH3+-like ion interacting with (G-C)4, (A-T)4, and [(G-C)·(A-T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH3+-like ion is near known alkylation sites. The results of the Az+ … [(G-C)·(A-T)]2 interaction are virtually identical to those found for the CH3+-like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G-C)·(A-T)]2.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 325-340 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of molecular orbital calculations, using MINDO/3 and CNDO/2L methods, have been used to characterize the chemical reaction of protonated aziridine with DNA nucleophilic base sites. The N-7 atom of guanine is found to be the preferred alkylation site only when the O-6 atom of guanine is involved in base-pair hydrogen bonding. Otherwise O-6 is the predicted major site of alkylation. This indirectly suggests that protonated aziridine alkylation processes involve base-paired DNA structures, since N-7 guanine is the observed major site of alkylation. Alkylation of N-3 adenine is predicted to be more favorable than chemical attack of the N-7 adenine position. Both of these sites, however, are predicted to be less reactive than N-7 of guanine. These chemical reactivity studies resolve alkylation specifically not achieved in the DNA-alkylator physical association calculations reported in the preceding paper.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 41 (1997), S. 37-50 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The torsion angle motions, generated from molecular dynamics (MD) simulations, of the two aliphatic chains of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) in its lipid monolayer were evaluated by comparing these motions to those of an equivalent isolated (free) n-alkane chain, and the same n-alkane chain in its crystal lattice. The time-dependent autocorrelation and (1,2)-, (1,3)-, (1,4)-, and (1,5)-cross-correlation functions were constructed to analyze the torsion angle motions. It was found that the torsion angle motions of the DMPC lipid monolayer aliphatic chains are intermediate to those of the free n-alkane chain and the same n-alkane chain in its crystal lattice, particularly for short correlation times. The torsion angle motions of the aliphatic chains of DMPC are also found to be essentially independent of the charge state on the head group. The linear aliphatic chains of a DMPC lipid monolayer behave most like the isolated n-alkane chains with respect to torsion angle flexibility, even though the pairs of aliphatic chains of each DMPC are part of an ordered monolayer assembly. The aliphatic chains of the DMPC molecules in their monolayer exhibit at least two types of wave motions. One of the wave motions is the same in form, though somewhat more diffuse, as a traveling wave found in n-alkane crystals. The other wave motion involves major torsion angle transitions, and has some characteristics of the soliton properties observed in n-alkane crystals near their respective melt transition temperatures. © 1997 John Wiley & Sons, Inc.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 12 (1973), S. 1197-1202 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Hoboken, NJ : Wiley-Blackwell
    Journal of Polymer Science: Macromolecular Reviews 13 (1978), S. 1-61 
    ISSN: 0076-2083
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Additional Material: 44 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Pharmaceutical research 15 (1998), S. 303-311 
    ISSN: 1573-904X
    Keywords: antiarrhythmics ; molecular dynamics ; partial least squares regression ; genetic function approximation ; quantitative structure-activity relationships
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Purpose. This study was done to explore the relationships of both macroscopic and molecular level physicochemical properties to in-vivo antiarrhythmic activity and interactions with phospholipid membranes for a set of cationic-amphiphilic analogs. Methods. The 4D-QSAR method, recently developed by Hopfinger and co-workers (1), was employed to establish 3D-QSAR/QSPR models. Molecular dynamics simulations provided the set of conformational ensembles which were analyzed using partial least squares regression in combination with the Genetic Function Approximation algorithm to construct QSAR and QSPR models. Results. Significant QSAR models for in-vivo antiarrhythmic activity were constructed in which logP (the partition coefficient), and specific grid cell occupancy (spatial) descriptors are the main activity correlates. LogP is the most significant QSAR descriptor. 4D-QSPR models were also developed for two analog-membrane interaction properties, the change in a membrane transition temperature and the ability of the analogs to displace adsorbed Ca2+-ions from phosphatidylserine mono-layers. Conclusions. Spatial features, represented by grid cell occupancy descriptors, supplement partition coefficient, which is the most important determinant of in-vivo antiarrhythmic activity, to provide a comprehensive model for drug action. The QSPR models are less significant in statistical measures, and limited to interpretation of possible molecular mechanisms of action.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 29-40 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The influence of inserting certain residues (X) into a polytripeptide sequence conformed into a poly-L-proline II helix is examined theoretically. It is found that for sequences such as -Gly-Pro-X- and -Gly-X-Pro-, the introduction of glycyl, L-alanyl or L-seryl residues in the X position destabilizes the helix so that it is no longer the most stable intramolecular form. On the other hand, L-prolyl and L-hydroxyprolyl residues cause the PP II helix to be most stable. Of the many stable intramolecular forms, the majority will not pack efficiently to form fiber or solid-state structures. The Rich-Crick and Ramachandran collagen model structures were examined in terms of a Gly-Pro-Ala sequence, the Ramachandran, one-hydrogen-bond structure, being the most stable. However, another triple-strand structure for (Gly-Pro-Ala)n, is much more energetically favorable. Hence, it may be concluded that none of the aforementioned is an entirely satisfactory collagen model. The new triple helix conformation proposed by Traub, Yonath, and Segal for (Gly-Pro-Pro) is found to give a more favorable intramolecular conformation for (Gly-Pro-Ala)n than those derived from other collagen models. It is concluded that the collagen molecule derives its stability from interchain interactions in proline-sparse regions and intrachain stability in proline-rich regions.
    Additional Material: 2 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 10 (1971), S. 1299-1315 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interchain energetics of alpha, beta, and PGII conformations of polyglycine, the PPII and left-handed 3.30 fold helical conformations of trans poly-L-proline, and the Yonath and Traub triple helix and left-handed three fold helices of poly(gly-pro-pro) were investigated. Intra- and inter-chain stabilization energies appear to be inversely related, and the interchain stabilization energy can be as large its the intrachain energy. The minimization of the interchain energy can be described by the simultaneous optimization of interchain hydrogen bonding and intermolecular-sidechain digitation. The stability of the poly(gly-pro-pro) triple helix can be readily explained in terms of these two factors. In all cases the experimentally observed lattice packing is predicted, although the calculated lattice constants are slightly larger than those observed. The small differences between observed and predicted lattice constants probably reflect small errors in present conformational potential functions. Homopolymers are probably the best systems to use in the refinement of conformational potential functions because solvent effects arc minimized and the experimentally observed lattice constants provide a check on the configurational calculations.
    Additional Material: 3 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 377-388 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular dynamics (MD) simulations to model possible reaction pathways of the dynemicin-A-DNA cleavage mechanism were performed. Two base-pairs sequences, ApCpTp-ApCpTp-3′/TpGpApTpGpAp-5′ and CpApCpGpGpGp-3′/GpTpGpCpCpCp-5′, were considered in the calculations. A model based on a prior study of intercalation of dynemicin-A and posterior activation of the drug was assumed in this study. The minimum energy minor groove intercalation complexes for dynemicin-A were used as starting structures in the MD simulations for the reactive intermediate species involved in the postulated action mechanism. The dynemicin-A diol derivative product of the opening of the epoxy ring was used as a “steric mimic” ligand for the DNA-reactive diaryl intermediate. The calculated changes in the geometry of the intercalation complex, due to the opening of the epoxy ring, correspond to the approach of the postulated intermolecular reaction centers in the intercalation states that are responsible for the highest observed DNA cleavage frequency observed. Conversely, unfavorable reaction geometries were found for the intercalation modes corresponding to the lowest observed DNA cutting frequencies. © 1993 John Wiley & Sons, Inc.
    Additional Material: 13 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 12 (1973), S. 157-161 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A semi-empirical conformational energy calculation has been performed on the ionizable polydipeptide poly(Glu-Ala). The results indicate that; (1)the ionized polymer assumes the lefthanded extended helix conformation is aqueous solution; (2) the poly(Glu-Ala) extended helix is less stable than that of polyglutamic acid; (3) the unionized polydipeptide will preferentially assume the “β-helical” conformation (isolated 21 degenerate helix) in aqueous solution. These conclusions are supported by experiment.
    Additional Material: 1 Ill.
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