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  • 1
    Electronic Resource
    Electronic Resource
    Theoretical study of the binding of aliphatic diamines to the minor groove of a B-DNA (dA-dT)11 oligomer (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 1527-1542 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Theoretical computations are performed on the binding of aliphatic diamines +H3N-(CH2)n-NH3+ (n = 3-7), to the minor groove of a (dA-dT)11 oligomer held in the B-DNA conformation. The computations are performed in the framework of an additive procedure elaborated recently in this laboratory by means of which the intermolecular DNA-diamine interaction energies and the intramolecular energy variations of the diamine are computed simultaneously. The results of the computations show that the binding of the diamines occurs in well-defined configurations in which each cationic extremity interacts with specific sites, O2(T), N3(A), and O1,(S) in the groove, the overall configuration differing according to the length of the diamine. The overall energy balance for complexation is found to depend on the chain length of the diamine, an optimal value for δE being found for 1,6 diaminohexane. This result is discussed in light of available experimental results of the compared affinities of diamines for the double-stranded polymer dA-dT.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360240809
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  • 2
    Electronic Resource
    Electronic Resource
    Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents - A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 405-425 
    Details
    ISSN: 0006-3525
    Keywords: conformation ; alanyl dipeptide ; oligopeptides ; solvation ; SIBFA ; SCF/MP2 ; density functional theory ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A φ/ψ conformational energy map of a model alanyl dipeptide is first drawn using the SIBFA (Sum of Interactions Between Fragments Ab initio computed) procedure [N. Gresh, P. Claverie and A. Pullman (1979) International Journal of Quantum Chemistry Symposium, Vol. 13, pp. 243-253; N. Gresh, P. Claverie and A. Pullman (1982) International Journal of Quantum Chemistry, Vol. 22, pp. 199-215; N. Gresh, P. Claverie and A. Pullman (1984) Theoretical Chimica Acta, Vol. 66, pp. 1-20; N. Gresh, P. Claverie and A. Pullman (1985) Theoretical Chimica Acta, Vol. 67, pp. 11-32; N. Gresh, A. Pullman and P. Claverie (1985) International Journal of Quantum Chemistry, Vol. 28, pp. 757-771; N. Gresh, P. Claverie and A. Pullman (1986) International Journal of Quantum Chemistry, Vol. 29, pp. 101-118; N. Gresh (1995) Journal of Computational Chemistry, Vol. 16, pp. 856-882; N. Gresh and D.R. Garmer (1996) Journal of Computational Chemistry, Vol. 17, pp. 1481-1495; N. Gresh, M. Leboeuf and D.R. Salahub (1994) in Modelling the Hydrogen Bond, Vol. 569, American Chemical Society Symposia, Smith, D.A., Ed., pp. 82-112; N. Gresh (1997) Journal de Chim.-Phys. (Paris), Vol. 94, pp. 1365-1416]. A new formulation of the intramolecular (conformational) energy is used, consistent with the refinements that were recently published for the intermolecular interaction energies in joint SIBFA/ab initio supermolecule Self-Consistent Field/Moller-Plesset (SCF/MP2) and Density Functional Theory (DFT) studies of cation-ligand [see Gresh (1995) and Gresh and Garmer (1996) above], and H-bonded [see Gresh et al. (1994) above] complexes. The accuracy of the procedure is assessed, on fourteen conformers selected from the map, by comparing their relative conformational energies with those obtained from SCF/MP2 and DFT computations. Conformational energy maps are then recomputed in the presence of water, dimethyl sulfoxide, chloroform, and carbon tetrachloride, the solvation energies being computed with the Continuum reaction field procedure due to J. Langlet et al. [(1988) Journal of Physical Chemistry, Vol. 92, pp. 1617-1631], and recently integrated into SIBFA [J. Langlet, N. Gresh and C. Giessner-Prettre (1995) Biopolymers, Vol. 36, pp. 765-780]. Such an integrated procedure is next extended to a comparison of the relative stabilities of, on the one hand, the competing types of β-turns (I, I′, II, II′) that are prevalent in Ala/Gly-based model tetrapeptides, and, on the other hand, α- vs 310-helices in alanine oligomers. © 1998 John Wiley & Sons, Inc. Biopoly 45: 405-425, 1998
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Thermolysin-inhibitor binding: Effect of the His231 → Ala mutation on the relative affinities of thiolate versus phosphoramidate inhibitors - a model theoretical investigation incorporating a continuum reaction field hydration model (1997)
    New York : Wiley-Blackwell
    Biopolymers 41 (1997), S. 145-164 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of site-directed mutagenesis experiments have been performed in our laboratory, bearing on the Zn2+ metalloprotease from Bacillus stearothermophillus, a protein very closely related to thermolysin (TLN), and their consequences on the binding of inhibitors belonging to the thiolate, carboxylate, hydroxamate, and phosphoramidate classes of compounds [A. Beaumont et al. (1995), J. Biol. Chem., Vol. 270, pp. 16803-16808]. An unexpected result related to the mutation of protonated His231, which resides at the entrance of the enzymatic cavity, into an Ala residue, shown to leave the binding affinities of thiolate inhibitors unaffected, but to abolish almost completely those of the phosphoramidate inhibitors. In order to account for such contrasting differential responses, we have undertaken a theoretical study of the comparative binding affinities of a representative thiol inhibitor, thiorphan (I) and a phosphoramidate (II), to a model of the enzymatic cavity of both the native and the mutated protein, encompassing up to 27 residues. The computations of inter- (ΔE) and intramolecular interactions were done with the sum of interactions between fragments ab initio computed procedure [N. Gresh et al. (1984), Theoret. Chim. Acta. Vol. 66, pp. 1-20; (1985), Theoret. Chim. Acta, Vol. 67, pp. 11-32; (1986), Int. J. Quant. Chem., Vol. 29, pp. 101-118; (1994), in Modelling the Hydrogen Bond, American Chemical Society Symposia, Vol. 569, D. A. Smith, Ed., American Chemical Society, pp. 82-112; N. Gresh (1995), J. Comput. Chem., Vol. 16, 856-882]. The energy balances for the His231 → Ala mutation incorporate a solvation energy contribution, computed using the Langlet et al. Continuum procedure [J. Langlet et al. (1988), J. Phys. Chem., Vol. 92, pp. 1617-1631], and this term was shown to play a decisive role in the comparative energy balances of the thiolate vs phosphoramidate inhibitors. Whereas the resolvation energy was able to compensate for the loss of ΔE induced by the H231 A mutation for the complex of I, thus accounting for its insensitivity to the mutation, such a compensation did not occur in the case of II, leading in its complexes to an overall loss of about 7 kcal/mole in the mutated cavity with respect to the native one. These results emphasized the critical role played by solvation in enzyme-inhibitor recognition processses. © 1997 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    A theoretical exploration of conformational aspects of ethidium bromide intercalation into a d(CpG)2 minihelix (1987)
    New York : Wiley-Blackwell
    Biopolymers 26 (1987), S. 831-848 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to gain insight into the structural and conformational factors involved in the binding of ethidium bromide to oligonucleotides, theoretical computations are performed on the ethidium bromide-d(CpG)2 complexes, in which the ligand-nucleotide interaction energy, the conformational energy of the ligand, and that of the nucleotide are simultaneously optimized. The intermolecular and conformational energy computations are performed with the SIBFA procedures (sum of interactions between fragments computed ab initio), which use empirical formulas based on ab initio SCF (Self Consistent Field) computations. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structure) elaborated by Miller and co-workers. The pyrimidine sugar is held in the C3′-endo conformation and the purine sugar in the C2′-endo conformation in conformity with both x-ray and nmr results for dinucleoside duplexes. Several candidate intercalation sites, selected on the basis of energy criteria, could be generated by the procedure. They were found to recur in a persistent fashion over the whole range of unwinding angles investigated, which span from -20° to -30°. Among these, a conformation closely similar to the one determined crystallographically by Sobell et al. was found to be the intrinsically most favorable and to react with the strongest interaction energy with ethidium. For this conformation, the most favorable value of the unwinding angle is -26°, close to the value in the crystal structure. Several pairwise correlations of structural parameters could be evidenced. The effect of the 2′OH groups (as in RNA duplexes as opposed to DNA duplexes) was also investigated and shown to further enhance, albeit slightly, the intrinsic stability of the Sobell-like Δα = -26° conformation.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360260605
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  • 5
    Electronic Resource
    Electronic Resource
    A theoretical investigation of the intercalative binding of 7-H pyrido[4.3C]carbazole chromophore into a d(CpG)2 minihelix (1989)
    New York : Wiley-Blackwell
    Biopolymers 28 (1989), S. 835-849 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Theoretical computations are performed of the intercalative binding to a model d(CpG)2 minihelix of 7-H pyrido[4.3C]carbazole, the precursor of the antitumor bisintercalating drug ditercalinium. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structures) of Miller and co-workers. The ligand-nucleotide interactions and the nucleotide conformational energies are computed with the SIBFA procedures (sum of interactions between fragments ab intio computed), which use formulas of empirical origin that reproduce ab initio SCF (self-consistent field) computations. Among the candidate intercalation sites most favored energetically, one has a pattern of conformational angles related to the one determined crystallographically by Sobell et al. in a series of x-ray structural studies of small intercalator-dinucleotide monophosphate complexes. Optimal values of the unwinding angle, found in the range of -12° to -14°, are consistent with available experimental data on DNA.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360280405
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  • 6
    Electronic Resource
    Electronic Resource
    Binding of nogalamycin to model tetranucleotides (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 1491-1517 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intercalated complexes of the antitumor antibiotic nogalamycin (NGM) with the double-stranded oligonucleotides d(GCGC)2, d(ATAT)2, and d(ACAC) · d(GTGT) are investigated with the theoretical method SIBFA. The amino sugar part of the drug locates preferentially in the minor groove. An intrinsic preference for the d(ATAT)2 sequence over the d(ACAC) · d(GTGT) and d(GCGC)2 sequences is obtained, corresponding to relative energies 0, 11, and 15 kcal/mole, respectively. A mixed sugar-puckering pattern is preferred in the d(ATAT)2 complex while a uniform sugar-puckering pattern is preferred for the other sequences. No direct specific interaction involves the N+ - H part of protonated NGM. The location of the amino sugar as well as the sequence selectivity is due to the global electrostatic interaction of the dimethylammonium group with the given groove. The two hydroxyl groups of the amino sugar and the carbonyl of the carbomethoxy group encounter partners for hydrogen bonding at the intercalation site, but these interactions do not appear to govern the base sequence selectivity. The nogalose part is not found to be directly involved in the binding or in the selectivity. The conformations of isolated and intercalated NGM are discussed.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270913
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