Nucleotides, conformation

Rao, B. D. N. Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) smdies of nucleotide conformations in creatine kinase complexes effects due to weak nonspedftc binding. Biochemistry 1993,... 

For poly(dG-dC) with alternating guanine and cytosine sequence, a right-handed B-DNA form prevails at low salt conditions, whereas at higher salt concentrations a change occurs to a left-handed form called Z-DNA [661, 662]. In Z-DNA, the G C base pairs are again of the Watson-Crick type and the two polynucleotide strands are antiparallel, but the nucleotide conformations are different (Box 20.1). 

Yathindra N, Sundaralingam M (1973) Correlations between the backbone and side chain conformations in 5 -nucleotides. The concept of a rigid nucleotide conformation. Biopolymers 12 297-314... 

Gautier A. Phosphate mimic of nucleotides, conformational influences on the ribofuranose conformations. Heterocycles 2006 67 823-837. 

P-A combination of solid-state and NMR, X-ray diffraction, and model building is used to show that the B and C forms of fibrous macromolecular DNA consist of two distinct nucleotide conformations, which correspond closely to the BI and BII nucleotide conformations known from oligonucleotide crystals. 

A large number of stable conformations of both natural and synthetic DNA have been observed. They may be characterized in terms of gross structural parameters such as N, the number of molecular asymmetric units in K turns of the helix h, the axial rise per residue and r, the axial rotation per residue. Both right- and left-handed helices have been observed [13, 43]. In typical cases the molecular asymmetric unit is a mononucleotide but dinucleotide asymmetric units have been found in molecules in which the chemical repeat consists of two nucleotides [11]. The nucleotide conformations can be related to the different helical parameters both in terms of the backbone and conformational angles and features such as the sugar pucker and the base-pair displacement and orientation with respect to the helix axis. 

Figure 1.75 Z-form DNA results from wholesale conformational changes in deoxyguanosine nucleotide (dpG) residues. The more usual anti, +sc, C2 endo nucleotide conformation gives way to a syn, ap, C3 endo conformation, (a) Illustration of syn dpG conformation, (b) Ball and stick depiction of pdG(syn, ap, C3 endoj.pdC base pair as found in Z-form DNA.

The system of nomenclature for describing nucleotide conformations recommended at a previous Jerusalem Symposium (Sundaralingam et ai,... 

Further experimental and theoretical analyses of nucleotide conformations are foimd in E.D.Bergmann B.Pullman (eds.). Conformation of Biological Molecules and Polymers. Jerusalem Sysposla on Quantum Chemistry Biochemistry, vol.5 (1973), pp.209-467. 

Nucleotides, in many cases as their metal ion complexes, are involved in a great variety of enzymatic reactions either as substrates or as cofactors. In addition they may be viewed as the monomers of DNA and RNA. Lanthanide complexes of nucleotides have been extensively studied by R.J.P. Williams and his coworkers at Oxford. The interest in these complexes is two fold. The nucleotide conformation in solution can be elucidated by NMR from lanthanide induced chemical shifts and line-broadenings, (Barry et al., 1971). Lanthanide-nucleotide complexes may act as competitive inhibitors in enzymatic reactions, (Tanswell et al., 1974), and can be used as paramagnetic probes in the mapping of their binding site on the enzyme, (Tanswell et al., 1976). 

The main feature of the Z-form [84 Rl] in terms of energetics is that the repeated unit contains two nucleotides instead of one nucleotide as in the classical A- and B-forms. In each of the two polynucleotide chains there is a strict alternation of the nucleotide conformations (sy and anti for further details see chapter 2). 

Elmahdaoui, L., Tajmirriahi, H. (1995). A Comparative-study Of Atp and Gtp com-plexation with trivalent Al, Ga and Fe cations -Determination of cation-binding site and nucleotide conformation by FTIR difference spectroscopy. Journal of Biomolecular Structure and Dynamics, 13, 69. 

In classifying spatial relations, one must consider two types of nucleotide pairs adjacent and non-adjacent. Nitrogen base spatial relations are thus of three types adjacent-stacked (helical and non-helical), adjacent-unstacked, and non-adjacent-paired (see Figure 3). Nitrogen base spatial relations can efficiently be extracted from previously determined three-dimensional structures, stored and organized in a database, and applied to position and orient rigid nucleotide conformations. 

Although the conformational space of RNA three-dimensional structures is mainly constrained by nitrogen base spatial relations, the ribose and phosphate groups still allow one to prune several inconsistent conformations. In MC-SYM, the appending of nucleotides in a three-dimensional structure is performed by applying the nitrogen base transformations directly to the atomic coordinates of rigid nucleotide conformations. 

In the MC-SYM structural databases, the spatial relations and nucleotide conformations are stored in lists. The lists are sorted so that any sublist of the first n elements represents the most efficient sampling of the addressed space. This property is achieved by selecting as the first element of a list, the one that minimizes the sum of the square distances with all other elements. This element is considered the most common example of the given relational or conformational list. The next element to insert in the list is the one that maximizes the difference with all previously included elements. This sorting method supposes the existence of distance metrics to evaluate the difference between two spatial relations or nucleotide conformations. The following metrics gave good results in practice. 

A simple metric to measure the distance between two nucleotide conformations is to compute the rms deviation between the heavy atoms in the backbone of the two nucleotides when their nitrogen bases are superimposed. A variant of this metric consists in calculating the distance between the phosphate atoms only. This allows one to avoid the potential counterbalancing effect of the sugar pucker modes and backbone torsion angles. 

The MC-SYM structural database was built from the extraction of spatial relations and nucleotide conformations in previously determined RNA three-dimensional structures. A computer program that automatically detects the three types of... 

Figure 9 The 785-797 loop of I6S ribosomal RNA. (a) Secondary structure deduced from NMR data and a spanning tree. The arrow.s indicate the selected edges in the spanning tree, (b) MC-SYM. script corresponding to the spanning tree in (a). The ANYJ NT list contains combinations of C3 -, Clf-endo and anti nucleotide conformations...

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