Biomedical subjects
Publications and source records attributed to R Lavery.
Molecular modeling is used to study the opening pathways of bases within a B-DNA oligomer. It is demonstrated that many open states are possible for a single base pair, although a preference for opening towards the major groove of the double helix is found. In addition we show that opening is strongly influenced by the nature of the base involved and is also coupled in many cases to DNA bending.
Molecular modeling is used to study the sequence dependence of conformation and stability within helically regular duplex Z-DNA. The variations of conformation that are found are sufficiently important to be classified as a new type of polymorphism within the Z family. It is also demonstrated that certain sequences can adopt more than one of these polymorphic forms. Comparison with experimental studies of chemical reactivity within a natural DNA fragment, forced into a left-handed conformation, suggests that the results of our modeling may be used to explain the chemical reactivity observed. Comparison of the Z results with similar studies of the B form allow enthalpies of transition to be calculated as a function of base sequence.
We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinates of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.
The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.
A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.
Base sequence effects within double stranded RNA oligomers of A and Z conformations have been studied by molecular modeling using a methodological approach specifically adapted to nucleic acids. Calculations on symmetric oligomers having homonucleotide or dinucleotide repeating base sequences show that sequence changes can produce modifications in overall conformation, influence the degree of internal hydrogen bonding and strongly affect stability.
Closed circular DNA containing polypurine-polypyrimidine sequences can adopt a triple helical stem-loop structure under supercoiling pressure. We describe an automated procedure for building model loops and its application to the investigation of the polypyrimidine loop at the end of such a triple helical stem. All possible combinations of 3'-stacked and 5'-stacked structures have been examined for loops containing three, four, five, and six nucleotides. The lowest energy conformation is a four-membered loop with all bases stacked on the strand at the 3' end of the loop. The model predicts that sequences (GA)n, (GGGA)n and (GAAA)n should form the stem-loop structure more easily than (GGA)n and (GAA)n. It is also predicted that when a polypurine-polypyrimidine sequence converts from a double stranded structure to a triple stranded stem-loop, the most favorable conditions are those where an even number of basepairs makes the transition. Experimental tests of these predictions are also described.
Oligodeoxynucleotides can be synthesized by using the alpha anomers of nucleoside units. Oligo-alpha-deoxynucleotides are resistant to nucleases and could be used to regulate gene expression in vivo. Theoretical calculations were carried out to determine the conformational energy of an oligomeric alpha-beta duplex (dA)5.(dT)5 where the adenosine strand contains natural beta-deoxyribonucleotides and the thymidine strand contains synthetic alpha-deoxyribonucleotides. These calculations predict that in the more stable B-like conformation the two strands of the double helix should run parallel to each other whereas in the more stable A-like conformation the two strands should adopt an antiparallel orientation. In order to test these predictions 1,10-phenanthroline was covalently attached to the 5'-end of an alpha-octathymidylate. In the presence of copper ions and a reducing agent (beta-mercaptopropionic acid), the (phenanthroline)2-copper complex generates OH. radicals that cleave phosphodiester bonds in the complementary sequence to which the alpha-octathymidylate is bound. By use of a 27mer oligo-beta-deoxynucleotide containing an octadeoxyadenylate sequence as a target for the phenanthroline-substituted alpha-(dT)8, cleavage was observed on the 5'-side of the (dA)8 sequence, demonstrating that the alpha-beta DNA-DNA hybrid formed a double helix with parallel orientation of the two strands. The same result was obtained when alpha-(dT)8 was bound to beta-(dA)n with n = 8 or 10. When a beta-oligoriboadenylate was used as a target, cleavage occurred exclusively on the 3'-side of the (rA)8 or (rA)10 sequence, indicating that the alpha-beta DNA-RNA hybrid formed a double helix with an antiparallel orientation of the two strands. When a phenanthroline-substituted beta-octathymidylate was used instead of the alpha-octathymidylate, an antiparallel double helix was formed independently of whether the target beta sequence was a DNA or an RNA.
The pathway for base pair opening within a B-DNA duplex is investigated by theoretical molecular modeling. The results show that the disruption of a single base pair is energetically compatible with the deductions made from hydrogen exchange measurements. In addition, it is found that the opening process is greatly facilitated by DNA bending and that, conversely, once a base pair is disrupted, DNA can bend very easily. It appears that the energetic coupling between these two processes may play an important role in many biological reactions involving nucleic acid distortion.
An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is shown that this approach can be applied equally easily to single or double stranded nucleic acids. The results of this analysis yield both the absolute helicoidal parameters of individual bases/base pairs and the relative helicoidal parameters between successive bases/base pairs as well as the overall locus of the helical axis. The possibilities of this mathematical approach are demonstrated with the help of a computer program termed "Curves" which is applied to the study of a number of different nucleic acid structures.
A theoretical study is presented on the binding to B-DNA of a series of lexitropsins, these ligands being netropsin derivatives in which one or both of the pyrrole rings have been replaced by imidazoles. The best complexes have been located by energy minimisation taking into account nucleic acid flexibility, ligand flexibility, explicit, mobile counterions and solvent dielectric effects. Calculations have been performed for two homopolymeric DNA receptor sequences, AT base sequence, which only decreases in the imidazole derivatives. These results emphasize the decisive role of the molecular electrostatic potential of the nucleic acid in determining the sequence selectivity of these ligands, as opposed to the postulated role of adenine C2 - pyrrole beta hydrogen contacts.
Interactions between B-DNA and homopolymeric alpha-helices of glycine, alanine, serine, asparagine and aspartic acid have been studied theoretically. The complexation energy has been minimised taking into account the interactions between DNA and the polypeptides as well as the internal energy of the alpha-helix and the interaction energy of counterions with the complex. The results obtained indicate the important role of strong hydrogen bonds between the peptide side chains and nucleic acid phosphate groups, these bonds being much stronger than specific interactions with the base-pairs. The formation of these structural bonds depends on the size of the alpha-helix, which in turn determines whether bridging across the major groove is possible. The steric role of the methyl group of thymine in orienting the peptide helix and the role of DNA screening cations in complex stabilization are also significant.
Using the stopped-flow kinetic method we have measured the deuteration rate of the amino protons in 2'deoxyguanosine 5'monophosphate and 7-methylguanosine 5'monophosphate. For both compounds the exchange rates are accelerated with increasing concentration of a large number of buffers with widely differing pKs. The results obtained, in conjunction with a theoretical model study, give rise to serious doubts concerning the normally accepted mechanism of amino proton exchange involving a pre-protonation at N7.
A general and efficient methodology is presented which allows molecules containing one or many rings of any size to be manipulated within energy minimization procedures. Variables describing the conformation of the molecules concerned are limited to dihedral and ring valence angles and the ring closure conditions are treated as equality constraints. An application is made to the ion transporter valinomycin and its complexes with K+ and Na+ which illustrates the possibilities of the approach and leads to results which allow a better understanding of the conformational mechanics of this important ionophore.
A novel and powerful methodology is developed which allows the alteration of molecular structures subjected to constraints and its application to polynucleotides with mononucleotide repeat symmetry, including the treatment of the flexible sugar rings is described. In contrast to procedures proposed by other authors, the constraints are formulated as differential equations which are linear with respect to the differentials of the geometrical variables. These equations can be solved easily by stepwise numerical integration involving sucessive infinitesimal rotations (SIR). Moreover, these equations define a set of independent curvilinear coordinates which can be used directly as the parameters of the energy functional in an energy minimisation procedure. This methodology allows the scanning of the full configurational space of a complex macromolecule, with direct access to the helicoidal variables in the case of periodic systems. Through this approach many problems involving biomacromolecular conformation, which would otherwise be intractable, may be studied with considerable ease.
Results concerning the flexibility of mononucleotide repeat DNA are presented using a novel methodology, denoted "SIR", to describe continuous changes in the structure of the nucleic acid. This methodology, combined with internal energy calculations and analytical energy gradients allows us to determine optimal conformations of poly(dG).poly(dC) and poly (dA).poly(dT) in both the A and B forms, taking into account the influence of the solvent medium and explicit counterions. Subsequently, several different types of distorsion of these optimal structures are investigated. It is shown that excellent correlation with experimental results concerning coupled changes in structural variables is obtained and several new correlations are also detected.
A theoretical modelling of the interaction of putrescine (H3+N-(CH2)4-(+NH3) with DNA is carried out, introducing two new features which make the simulation of this interaction considerably more realistic. Firstly, the DNA to which putrescine is bound is fully flexible and thus able to respond to the distorting influence of the ligand. Secondly, the effect of changing the ratio of DNA base pairs per bound ligand is explicitly modelled. In this way, we have been able to confirm the experimentally known preference of putrescine binding with AT base pairs in B-DNA, but we also show, through the new features introduced, that the nature of the binding site of the ligand and the resulting impact on DNA conformation is strongly modified by the ligand binding density.
A detailed theoretical study has been made for five antibiotics which all bind selectively to AT sequences in the minor groove of B-DNA: SN-18071, NSC-101327, distamycin-2, distamycin-3 and netropsin. The optimal complexes were found for systems in which the flexibility of DNA, as well as that of the antibiotics, was taken into account. Explicit, mobile counterions and a dielectric function modelling aqueous solution were also included. The binding geometries of the most strongly interacting antibiotics, distamycin-3 and netropsin, are compared in considerable detail and it is shown that notable differences exist between them. The results for netropsin are also discussed in the light of recent disagreements concerning its exact binding location within DNA.