An exploratory ab initio conformational analysis of selected fragments of nicotinamide adenine dinucleotide (NAD+). Part II: adenosine

Electron Paramagnetic Resonance and Electron Spin Echo Studies of Co2+ Coordination by Nicotinamide Adenine Dinucleotide (NAD+) in Water Solution

Co²⁺ binding to the nicotinamide adenine dinucleotide (NAD⁺) molecule in water solution was studied by electron paramagnetic resonance (EPR) and electron spin echo at low temperatures. Cobalt is coordinated by NAD⁺ when the metal is in excess only, but even in such conditions, the Co/NAD⁺ complexes coexist with Co(H₂O)₆ complexes. EPR spin-Hamiltonian parameters of the Co/NAD⁺ complex at 6 K are g_z  = 2.01, g_x  = 2.38, g_y  = 3.06, A_z  = 94 × 10^-4 cm^-1, A_x  = 33 × 10^-4 cm^-1 and A_y  = 71 × 10^-4 cm^-1. They indicate the low-spin Co²⁺ configuration with S = 1/2. Electron spin echo envelope modulation spectroscopy with Fourier transform of the modulated spin echo decay shows a strong coordination by nitrogen atoms and excludes the coordination by phosphate and/or amide groups. Thus, Co²⁺ ion is coordinated in pseudo-tetrahedral geometry by four nitrogen atoms of adenine rings of two NAD⁺ molecules.

Conformational diversity of ligands bound to proteins

The phenomenon of molecular recognition, which underpins almost all biological processes, is dynamic, complex and subtle. Establishing an interaction between a pair of molecules involves mutual structural rearrangements guided by a highly convoluted energy landscape, the accurate mapping of which continues to elude us. Increased understanding of the degree to which the conformational space of a ligand is restricted upon binding may have important implications for docking studies, structure refinement and for function prediction methods based on geometrical comparisons of ligands or their binding sites. Here, we present an analysis of the conformational variability exhibited by three of the most ubiquitous biological ligands in nature, ATP, NAD and FAD. First, we demonstrate qualitatively that these ligands bind to proteins in widely varying conformations, including several cases in which parts of the molecule assume energetically unfavourable orientations. Next, by comparing the distribution of bound ligand shapes with the set of all possible molecular conformations, we provide a quantitative assessment of previous observations that ligands tend to unfold when binding to proteins. We show that, while extended forms of ligands are indeed common in ligand-protein structures, instances of ligands in almost maximally compact arrangements can also be found. Thirdly, we compare the conformational variation in two sets of ligand molecules, those bound to homologous proteins, and those bound to unrelated proteins. Although most superfamilies bind ligands in a fairly conserved manner, we find several cases in which significant variation in ligand configuration is observed.