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We present the results of molecular dynamics simulations on base paired deoxyribonucleotides dA10·dT10, d(GCGCGCGCGC)2d(ATATATATAT)2d(CGCGA)·d(TCACG) (AC mismatch) and d(CGAGA)·d(TCGCG) (GA mismatch). The average structural properties — helix parameters, H‐bond parameters, sugar puckers, torsional angles, root mean square atomic fluctuations — are compared to those found in earlier studies on the sequence d(CGCGA)·d(TCGCG).1The properties of the decamer helices remain B DNA like throughout the simulation, confirming our inference1that a model which treats solvent/counterions in a simple fashion (full charge on phosphates, but use of large hydrated counterions and a distance dependent dielectric constant) is a reasonable “first order” model to simulate the properties of DNA helices over periods of at least 100 psec. There are a number of sequence dependent effects observed in the three decanucleotides studied here, among them differences in H‐bond properties, sugar pucker and helix repeat/base tilts. In d(GCGCGCGCGC)2and d(ATATATATAT)2the H‐bonds all stay near the classic Watson‐Crick distance and the base tilts and twists are small (10–20°). On the other hand, in dA10·dT10there are much larger deviations of H‐bonding from classic Watson‐Crick and H‐bond exchange during the simulation. There are many more examples of sugar repuckering in the AT decamers, and the relative frequency of such repuckering is qualitatively consistent with what one would expect based on molecular mechanics studies. A comparison of the torsional angles, sugar puckers, helical parameters, root mean square atom amplitudes and hydrogen bond parameters of the sequence d(CGCGA)·d(TCGCG) with the two mismatched analogues demonstrates that the effect of the poorer hydrogen bonding at the central base pair is transmitted throughout the sequence, leading to significantly greater root mean square fluctuations in all dihedral angles, significantly higher % of non‐“standard C2′ endo” sugar puckers, generally longer H‐bond distances, with greater % of “long” H bonds during the simulation, larger RMS amplitude of atomic fluctuations and greater helix twist and tilt of the base pairs. The average helix repeat is 9.0 for the AC mismatch, and 10.1 for the GA mismatch, compared to 10.0 for the normal sequence.

The side-chain conformations of psychoactive phenothiazine drugs in crystals are different from those of biologically inactive ring sulfoxide metabolites. This study examines the potential energies, molecular conformations and electrostatic potentials in chlorpromazine, levomepromazine (methotrimeprazine), their sulfoxide metabolites and methoxypromazine. The purpose of the study was to examine the significance of the different crystal conformations of active and inactive phenothiazine derivatives, and to determine why phenothiazine drugs lose most of their biological activity by sulfoxidation. Quantum mechanics and molecular mechanics calculations demonstrated that conformations with the side chain folded over the ring structure had lowest potential energy in vacuo, both in the drugs and in the sulfoxide metabolites. In the sulfoxides, side chain conformations corresponding to the crystal structure of chlorpromazine sulfoxide were characterized by stronger negative electrostatic potentials around the ring system than in the parent drugs. This may weaken the electrostatic interaction of sulfoxide metabolites with negatively charged domains in dopamine receptors, and cause the sulfoxides to be virtually inactive in dopamine receptor binding and related pharmacological tests.

Conformational energy calculations have been presented on guanine nucleoside in which the furanose ring is replaced by 2′,3′-dideoxy-2′,3′-didehydrofuran using molecular mechanics and conformational analysis. Conformational energies have been evaluated using the MM2 and AMBER94 force field parameters at two different dielectric constants. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (χ) and C4′-C5′ (γ) bonds torsions. In general, the χ-γinterrelationships differ from the corresponding plots for unmodified nucleosides and nucleotides, reported previously. Consistency of the calculated preferred conformations with the x-ray data is sensitive to the force field employed.

We present conformation energy calculations on the model dipeptide 1-acetylamino-N-methyl-2,5-cyclohexadiene-1-carboxamide (1) and its two derivatives in which the C-2 and C-6 of the cyclohexadiene ring are substituted. The energy calculations have been done using molecular mechanics methods with a force field derived from MM2. The salient features are expressed in terms of conformational energy plots, drawn as a function of the backbone torsion angles φ(C-N-Cα-C) and ψ(N-Cα-C-N). Two families of conformations are found to be the global minima in the (φ,ψ) space, one corresponding to a region with fully extended structures characterized by (φ,ψ) = (180° ± 20°, 180° ± 20°) and the other characterized by (φ,ψ) = (180° ± 20°, ± 60 ± 20°). The low energy structures of these model compounds are qualitatively consistent with the available amount of X-ray crystal structure data on peptidomimetics similar to 1. The salient results obtained have important implications on the design of constrained peptidomimetics with the above two conformations.

Site-directed mutagenesis is a very powerful approach to altering the biological functions of proteins, the structural stability of proteins and the interactions of proteins with other molecules. Several experimental studies in recent years have been directed at estimating the changes in catalytic properties, (rates of binding and catalysis) in site-directed mutants of enzymes compared to the native enzymes1–3. Simulation approaches to the study of complex molecules have also become more powerful, in no small measure owing to the increase in computer power4,5. These simulations have often allowed results of experiments to be rationalized and understood mechanistically. A new approach called the free-energy pertubation method, which uses statistical mechanics and molecular dynamics can often be used for quantitative calculation of free energy differences6. We have applied such a technique to calculate the differential free energy of binding and free energy of activation for catalysis of a tripeptide substrate by native subtilisin and a subtilisin mutant (Asn 155 → Ala 155). Our studies lead to a calculated difference in free energy of binding which is relatively small, but a calculated change in free energy of catalysis which is substantial. These energies are very close to those determined experimentally (J. A. Wells and D. A. Estell, personal communication), which were not known to us until the simulations were completed. This demonstrates the predictive power and utility of theoretical simulation methods in studies of the effects of site-specific mutagenesis on both enzyme binding and catalysis.

Peptides with conformationally restricted 1-aminocyclopropane-1-carboxylic acid (Acc3) moieties were previously shown to exhibit preference for γ-turn structures in the solution phase and solid phase. We present conformational energy calculations on model compounds containing 1-aminocycloalkane carboxylic acid with 4, 5, and 6-membered rings using molecular mechanics methods. The low-energy models adopt conformations characteristic of a variety of regular structures, such as the α-helix, γ-turn, and polyproline-II-type three- and four-fold helices. The energetically most favored models adopt the γ-turn (2.27helix) conformation in the model peptide of 1-aminocyclobutane-1-carboxylic acid (Acc4), similar to Acc3peptides, while they adopt the α-/310-helical conformation (of either handedness) in the corresponding compounds with cyclopentane (Acc5) and cyclohexane (Acc6). The salient features of our investigations are qualitatively consistent with the crystal structures of peptide analogs containing Acc4, Acc5, and Acc6and the previously reported solution phase and conformational studies on peptides containing Acc5. Our results have implications for the design of γ-turn and α-/310-helical peptidomimetics.

Conformational analysis of nucleic acids and polynucleotides is far more complex than that of proteins and polypeptides, due to five single bond rotations in addition to the sugar puckerings in the monomer. Sundaralingam1proposed the concept of the ‘rigid’ nucleotides from analysis of crystal structure data, with the flexibility allowed only about the phosphodiester bonds. However, the crystal structure of deoxyguanosine-5′–phosphate2,3indicates at gt conformation about the C-4′–C-5′ bond against gg in a conformationally rigid nudeotide1. Jack et al.4considered the flexibility of nucleotides in tRNA about the C-4′–C-5′ bond, thereby introducing the concept of ‘non-rigid’ ribonucleotides. Conformational flexibility of the f uranose ring in DNA and RNA and their energetics using classical and quantum chemical methods have been reported5–8. We have examined the flexibility of 3′-nucleotides. α, the most important of the conformational parameters defining the 3′-end of a nucleotide unit9, has a value in the range 195°–270° in all the 3′-nucleotides, dinucleoside monophosphates and higher oligomers which have been surveyed. A survey of the proposed structures of polyribonudeotides10,11also shows the values of a to be greater than 200°. However, the structures proposed for B-DNA by Arnott and Hukins12,13and D-DNA by Arnott et al.14have values of α of 155° and 141° respectively, much lower than the lowest observed value. The structure for B-DNA has two strong, short contacts (C-2′…OP-1 = 2.64 Å and HC-2″…OP-1 = 1.79 Å) which lead to an energetically unfavourable conformation. Hence, it is of interest to investigate whether, by allowing flexibility to the sugar moiety in the nucleotide unit, it is possible to make the structure energetically favourable. Here, conformational energy calculations were carried out to determine the range of α which would give rise to energetically favoured conformations with different sugar puckerings. Our analysis has shown that the theoretically obtained range is nearly the same as the preferred range in crystals, indicating the flexibility of the 3′-nucleotides.

We present molecular mechanics and molecular dynamics simulations on the dodecanucleotide d(CGCGAATTCGCG)2, incorporating a cis-synthymine–thymine cyclobutane dimer, represented as T[]T, at the TT site using the all atom force field. Although the starting optimized structures were essentially kink-free, kinked models are observed during the molecular dynamics simulations. Most conformational changes are seen in the sugar puckering and phosphodiester conformations of residues in and around the site of photolesion.

In the light of the biological significance of thymine photodimers, studies of the energetics of the dodecanucleotide fragment d(CGCGAATTCGCG)2 have been carried out using the methods of molecular mechanics, with and without incorporation of a thymine dimer in the cis-syn configuration. The results of the calculations suggest that the thymine dimerized structures show no gross distortion in the double helix with the conformational changes relative to the normal B-DNA double helix restricted largely to the dimer region. The energetics of dTp[ ]dT reveal a number of conformers which are energetically almost equally favorable and are, as a group, qualitatively consistent with NMR studies on this molecule. The biological omplications of the results of the conformational studies, reported here, have been examined vis-a-vis the currently available models for the recognition of DNA “damage” by repair enzymes.