A central partition of molecular conformational space. II. embedding 3D structures.

A combinatorial model of molecular conformational space that was previously developed, had the drawback that structures could not be properly embedded because it lacked explicit rotational symmetry. The problem can be circumvented by sorting the elementary 3D components of a molecular system into a finite set of classes that can be separately embedded. This also opens up the possibility of encoding the dynamical states into a graph structure.

A central partition of molecular conformational space. I. Basic structures.

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a 3x(N-1)-dimensional polytope. Conformations can be precisely located within the face hierarchy of the polytope, whose 1-skeleton provides the framework for determining paths between selected conformations.

Hamming distance geometry of a protein conformational space: application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core.

Protein structures can be encoded into binary sequences (Gabarro-Arpa et al., Comput Chem 2000;24:693-698) these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves.

Clustering of a molecular dynamics trajectory with a Hamming distance.

Based on the properties of discrete point arrangements we introduce the concept of dynamical activity, which allows one to formulate a simple double criterion for locating clusters of homologous conformers in a molecular dynamics trajectory.

Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations.

We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations.

Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution.

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair.

A molecular mechanics and dynamics study of alternate triple-helices involving the integrase-binding site of the HIV-1 virus and oligonucleotides having a 3'-3' internucleotide junction.

Triple helix formation by oligonucleotides can be extended beyond polypurine tracts with the help of specially designed linkers. In this paper we focus our attention on the integrase-binding site of the HIV-1 virus located on the U5 LTR end which contains two adjacent purine tracts on opposite strands. Two alternate triple helices with a 3'-3' junction in the third strand are considered: 5'-GGTTTTp3'-3'pTGTGT-5' and 5'-GGAAAAp3'-3'pAGAGA-5' The structural plausibility of these triplexes is investigated using molecular mechanics and dynamics simulations, both in vacuo and in aqua.

Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central C.A or A.G mismatch as a function of pH: nuclear magnetic resonance and molecular dynamics studies.

The DNA duplex 5' d(GCCACCAGCTC)-d(GAGCTGGTGGC) corresponds to the sequence 29 to 39 of the K-ras gene, which contains a hot spot for mutations. This has been studied by one and two-dimensional nuclear magnetic resonance, energy minimization and molecular dynamics. The results show that it adopts a globally B-DNA type structure.

About the large fluctuations observed using gas-phase molecular dynamics in the K-ras gene containing a mismatch.

We describe how we can reduce the periodic bending motions in the simulation in vacuo of the molecular dynamics of a short DNA fragment containing the Gly 12 hot spot of the K-ras oncogene and having at its center a mismatch CA+.

A database of 32 DNA triplets to study triple helices by molecular mechanics and dynamics.

We present here a database of 32 deoxyribonucleotide triplets, that can be used as building blocks of triple helix forming deoxyribonucleotides on a computer. This database is made of all the pairing schemes of the triplets ATT, GCC+, ATA and GCG where the third base forms two hydrogen bonds with the purine of the first two Watson-Crick strands. The essential features of the known triple helices were preserved in the resulting structures.

Object Command Language: a formalism to build molecular models and to analyze structural parameters in macromolecules, with applications to nucleic acids.

We have written a programming language OCL (Object Command Language) to solve, in a general way, two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecules: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes; and how to calculate standard or user-defined structural parameters that characterize the complex geometries of any macromolecule. OCL endows the user with three main capabilities: the definition of subsets of the macromolecule, called objects in OCL, with a formalism from elementary set theory or lexical analysis; the definition of sequences of elementary geometrical operations, called procedures in OCL, enabling one to build arbitrary three-dimensional (3D) orthonormal reference frames, to be associated with previously defined objects; and the transmission of these definitions to programs that allow one to display, to modify and to analyze interactively the molecular structure, or to programs that perform energy minimizations or molecular dynamics. Several applications to nucleic acids are presented.

The pH dependent configurations of the C.A mispair in DNA.

The structure of the cytosine-adenine mispair in a 7 base pair duplex has been investigated by proton NMR spectroscopy. At low pH, the predominant structure is protonated on the A residue and assumes a wobble conformation consistent with previous findings. The C residue of the mispair is found in a C2'-C3' endo equilibrium.

Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics.

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G.

The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics.

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three-dimensional solution structure of a 21 residue oligonucleotide capable of forming a hairpin structure with a loop of three thymidine residues. This structure is in equilibrium with a duplex form. At 33 degrees C, low ionic strength and in the presence of MgCl2 the hairpin form dominates in solution.

Molecular mechanics and dynamics of an abasic frameshift in DNA and comparison to NMR data.

In a previous publication (Ph. Cuniasse, L.C.

The GTm6AC sequence is overwound and bent.

By a combination of distance constraints obtained from NMR spectra and molecular mechanics calculations we have determined the three dimensional structure of the self-complementary decanucleotide d(CGCGTm6ACGCG). Methylation of an adenine at a position 3' to T induces significant conformational changes relative to B-DNA. This arises from the close proximity of the four methyl groups in the large groove in the centre of the sequence.

An algorithm for studying cooperative transitions in DNA.

Cooperative transitions in DNA (B to Z, B to A, helix to coil, etc.) are known to depend strongly on nucleotide sequence. In general the change in free energy involved in the transition can be expressed as: delta G(seq) = 2RT log (sigma) where sigma is a factor arising from the free energy associated with boundaries of different conformations along the molecule.

Promoter recognition and transcription initiation in E. coli.

Analysis of stability maps of sequences harbouring E. coli RNA polymerase promoters shows a characteristic splitting in homostable domains, despite the heterogeneity of the sequences. Correlation of stability maps with results from static approaches giving the contact points of the enzyme on promoters and functional studies employing abortive initiation assay allow us to propose a general mechanism for recognition of promoters and transcription start.

Local stability involved in characterizing and controlling promoters in eukaryotes.

Eukaryotic promoters with known in vivo activities have been analysed for characteristic stability patterns. Correlation of transcription yield in promoter mutants with size and stability of individual domains of the promoter stability profile supports the conclusion that eukaryotic promoters are built up by at least three elements: a region enabling the transcription ("enhancer"), with a characteristic stability pattern; an activator domain, with high GC content, whose activator potential is controlled by the domain stability and length; a trap domain, with high AT content, setting the cap site. The activated enzyme undergoes a steady deactivation process, losing half of its activity upon moving 55 bases between the activator and the trap site.

Physical characteristics in eucaryotic promoters.

For a series of wild type and mutated eucaryotic gene prelude sequences (mainly "promoters" of SV40 early gene (Benoist and Chambon, Nature 290, 304 (1981); Moreau et al., Nuc. Acids Res.

The hierarchical approach to the DNA stability problem. I. Patterns in non-equilibrium denaturation and renaturation.

As proposed by Azbel (Phys. Rev. Letters, 1973, 31, 589-592), DNA sequences may be uniquely divided into embedded segments with different lengths and stabilities, each of them a potential denaturation unit.

The hierarchical approach to the DNA stability problem. II. Some applications and speculations with yeast mitochondrial DNA as an example.

As discussed in the preceding article [1] hierarchical analysis of DNA sequences should make it possible to treat complex unfolding (and refolding) processes involving both equilibrium and non-equilibrium subtransitions. Hence a variety of actual experimental situations may be analyzed. This is demonstrated with the help of a 1950 bp yeast mitochondrial DNA sequence encompassing part of the 21S ribosomal RNA gene: excellent fit of complex denaturation and renaturation profiles is achieved with only two adjustable parameters.

Key for protein coding sequences identification: computer analysis of codon strategy.

The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed.

[Analysis of the stability and local cooperativity of DNA: proposal of a molecular mechanism for the initiation of the transcription of gene A3 of bacteriophage T7 by the RNA polymerase from E. coli].

RNA polymerase (RNAP) complexed to the A3 promoter of bacteriophage T7 is known to unwind a DNA segment located downstream of the Pribnow box. This finding can be accounted for if it is assumed that the subunit sigma of RNAP unstabilizes three GC base pairs located just upstream of the transcription start. As a consequence, the rate of promoter utilisation might be related to the relative stability of the DNA between the "Pribnow box" and the transcription start.

[Analysis of the stability and local cooperativity of DNA : elements permitting the recognition of promoters by DNA-dependent RNA polymerase].

Analysis of the local stability of promoters processed by E. Coli RNA polymerase shows that they bear a characteristic stability profile: two segments of low stability are located around --35 and --8 bases ahead of the transcription start and are generally bordered by more stable segments. This key profile may act as a recognition signal for both attracting and positioning the RNA polymerase in the promoter site.