Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate

  title={Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate},
  author={Janet M. Thornton and Peter M. Bayley},
A systematic study of the conformational states of the dinucleotide diadenosine 5′,5′‐pyrophosphate (AppA), an analog of the coenzyme NAD+, has been made using semi‐empirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The most stable structures exhibit stacking interactions between the adenine bases; there are many different stacked states of similar energy; their stability is derived from nonbonded… Expand
6 Citations
Conformational energy calculations for dinucleotide molecules: A study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+)
A study of the conformational states of the dinucleotide coenzyme NAD+ has been made using semiempirical energy calculations, and predictions correlate well with the available experimental data. Expand
Theoretical studies of nucleic acid conformation: potential energies, chain statistics, and model building
Theoretical investigations of nucleic acid conformation* attempt to find a rational connection between the chemical architecture of the polynucleotides and their macroscopic properties. The fieldExpand
What is the conformation of physiologically-active dinucleoside polyphosphates in solution? Conformational analysis of free dinucleoside polyphosphates by NMR and molecular dynamics simulations.
It is concluded that natural, free Np(n)N's at physiological pH exist mostly in a folded (stacked), rather than extended conformation, in several interconverting stacking modes. Expand
Base stacking in adenosine dimers revealed by femtosecond transient absorption spectroscopy.
Results show that the signature of these states in transient absorption experiments can be a more reliable diagnostic of base stacking than the occurrence of exciton-coupled CD signals, and draw attention to the important role the backbone plays in producing structures with axial (helical) chirality. Expand
Profile of Janet M. Thornton.
  • N. Zagorski
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2005
When Janet Thornton, a structural and computational biologist, first began analyzing protein structures in 1973, the structures for only a handful of proteins had been solved, and the genome for even the smallest virus was unknown. Expand


Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate.
The results for NMN+ suggest that a strong electrostatic interaction between the positively charged nicotinamide nitrogen atom and negatively charged phosphate oxygen is possible, stabilizing a few specific states, and will be most significant in a solvent-free situation or an apolar environment. Expand
Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate
As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. InExpand
Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base‐sugar units
In this paper, the preferred conformations of the bases with respect to the sugar in various base‐sugar units are worked out using criteria of potential energy. The van der Waals type of intercationsExpand
The conformation of pyridine dinucleotides in solution.
Abstract The dependence of chemical shifts in the nuclear magnetic resonance spectra of pyridine nucleotides on concentration, pH, and temperature has been examined. The data indicate that all of theExpand
Stereochemistry of nucleic acids and polynucleotides. V. Conformational energy of a ribose‐phosphale unit
The potential energy calculations on the sugar‐phosphate unit for different puckerings of the sugar are reported in this paper. The results obtained here essentially confirm our earlier predictionsExpand
The Conformation of Pyridine Nucleotides Studied by 31P and 1H Fast Fourier Transform Nuclear Magnetic Resonance Spectroscopy. II. The Backbone Conformation of Dinucleotides
Using parameters derived from the component mononucleotides, 13-NMN, 5'-AMP, and 5'-ADP, the "P n.m.r. spectra of oxidized pyridine coenzymes, recorded in the presence of coupling from the riboseExpand
Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond model
It is demonstrated that steric interactions alone are insufficient to account for the spatial characteristics of polynucleotide chains. Expand
Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono‐, di‐, tri‐, tetraphosphates, nucleic acids and polynucleotides
A uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect toExpand
Complementary studies on the rigidity‐flexibility of nucleotides
In view of investigating Sundaralingam’s proposal [ 1,2] of a “rigid” nucleotide conformation (anti about the quantum mechanical procedure PCILO the conforcyclic C(4’)-C(5’) bond) we have studiedExpand
The structure of the nicotinamide-adenine dinucleotide coenzyme when bound to lactate dehydrogenase.
The electron density distribution of M4 dogfish lactate dehydrogenase at 5 A resolution has been re-calculated using improved phases derived in part from a new heavy atom derivative. Difference mapsExpand