Solution NMR structure and dynamics of human apo-S100A1 protein

Abstract

S100A1 belongs to the EF-hand superfamily of calcium binding proteins. It is a representative of the S100 protein family based on amino acid sequence, three-dimensional structure, and biological function as a calcium signal transmitter. It is a homodimer of noncovalently bound subunits. S100A1, like most of other members of the S100 protein family, is a multifunctional, regulatory protein involved in a large variety of biological processes and closely associated with several human diseases. The three-dimensional structure of human apo-(i.e. calcium free)-S100A1 protein was determined by NMR spectroscopy (PDB 2L0P) and its backbone dynamics established by ¹⁵N magnetic relaxation. Comparison of these results with the structure and backbone dynamics previously determined for bovine apo-S100A1 protein modified by disulfide formation with β-mercaptoethanol at Cys 85 revealed that the secondary structure of both these proteins was almost identical, whereas the global structure of the latter was much more mobile than that of human apo-S100 protein. Differences between the structures of human and rat apo-S100A1 are also discussed.

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

“…Nevertheless, in both versions of apo-S100A1, a local hydrophobic cluster is formed, which includes side chains of aromatic residues Phe 88 , Phe 89 , and Trp 90 from one monomer together with the phenyl group of Tyr 26 located in the N-terminal Ca 2ϩ binding loop of the other subunit. Similar intersubunit NOE contacts that indicate an interaction between these protein sites have been detected previously in apo-S100A1 and its mixed disulfide forms (18,53). Another aromatic residue, Phe 44 , is the central residue of the linker region.…”

“…3). However, ⌬␦ tot values in those regions lie in the range of 0.1-0.35 ppm and are smaller than those previously observed between apo-S100A1 and apo-S100A1-␤ME forms (53). Alterations of backbone conformation upon S-nitrosylation were further confirmed by analysis of backbone mobility with the random coil index approach (54).…”

Selective diagonal-free 13C,13C-edited aliphatic–aromatic NOESY experiment with non-uniform sampling

“…The high resolution 3D structure based on the standard 3D 13 C- and 15 N-edited NOESY-HSQC spectra (Zhang et al 1994; Muhandiram et al 1993) is available in PDB under accession code 2LHL. Similarly to the native S100A1 (Nowakowski et al 2011), this protein mutant also exists in solution as a homodimer built up of noncovalently attached subunits (molecular weight of the monomer is 10 kDa). NMR sample contained 1.0 mM 15 N, 13 C labeled protein (the monomer concentration) in 90 %/10 % H 2 O/D 2 O, 50 mM TRIS-d 11 , 1.0 mM EDTA, 0.1 mM NaN 3 and 50 mM NaCl with pH adjusted to 7.2.…”

NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme

“…It should be pointed out that the conformational exchange mechanism can affect the apparent transverse relaxation rate only if Dd -0. The optimal model parameters were determined by the least squares procedure consisting of minimization through a grid search of the target function comprising the sum of the squared differences between the experimental values of the relaxation parameters and their model-derived counterparts (Stone et al, 1992;Nowakowski et al, 2011Nowakowski et al, , 2013 For the analysis of the relaxation data measured at a single magnetic field strength, the unfavorable observations to parameters ratio was taken into account. In order to reduce the number of parameters, the R 1 R 2 product as a function of amino acid sequence was used to separate residues exhibiting chemical exchange (group A) from those with R ex = 0 (group B).…”