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Changes of albumin secondary structure after palmitic acid binding : FT-IR spectroscopic study

Oleszko A, Hartwich J., Gąsior-Głogowska M., Olsztyńska-Janus S.

Acta of Bioengineering and Biomechanics

2018

Vol. 20, no. 1

59--64

Purpose: Albumin is an universal transport protein. Plasma pool of free fatty acids arising from triglyceride hydrolysis, critical in energy metabolism and etiology of metabolic disorders is transported by albumin. According to various studies albumin has from seven to nine binding sites with diverse affinity to long chain fatty acids. X-ray diffraction crystallography measurements have provided data only for pure human serum albumin or albumin with fully saturated binding sites. These results have shown that amount of -helices is higher after fatty acids binding. Molecular mechanics simulations suggest that binding of fatty acids in two high-affinity sites leads to major conformational changes in albumin structure. The aim of this research was to investigate albumin secondary structure upon gradually increasing fatty acids to protein mole ratio. Methods: Fourier transform infrared spectroscopy was applied to study changes of bovine serum albumin (as an analogue of human serum albumin) -helical structures after binding palmitic acid in a range of 0–20 palmitic acid: albumin molar ratios representing pure protein, partial, full saturation and excess binding sites capacity. Results: Amount of -helices was increasing along with the amount of palmitic acid: bovine serum albumin molar ratio and reached maximum value around 2 mol/mol. Conclusions: Our studies confirmed molecular mechanics simulations and crystallographic studies. Palmitic acid binding in two high-affinity sites leads to major structural changes, filling another sites only slightly influenced bovine serum albumin secondary structure. The systematic study of fatty acids and albumin interactions, using an experimental model mimicking metabolic disorders, may results in new tools for personalized nanopharmacotherapy.

Scoring matrix based on similarity of protein backbone dihedral angles

Pokuta W.

Metody Informatyki Stosowanej

2011

nr 3

137-149

The article describes the results of studies on the similarity of protein structures generated by the sequences differing by only one amino acid residue. On this basis, the table of amino acid residue similarities has been determined. Similar residue sequences should generate similar protein structures – on this basis act such classification systems as SCOP and CATH. These systems detect the existence of domains of different lengths in the sequences. These domains are characteristic for proteins which exist in organisms. Synthesized proteins are not related to any other proteins and may contain domains that can not be classified by traditional methods. The solution to this problem may be to analyzing all the possible combinations of amino acid residues and observation of secondary structures generated by this sequence in exising proteins. Analyzing the structural differences in the sequences differing only by one amino acid residue gives information on the structural similarity of these amino acids. The task of analyzing all possible combinations of amino acid sequence is possible only for short stretches, because for longer stretches the same sequence cannot be found in the existing databases. So the second question is: how long the sequence should be analyzed in order to enable determining the local backbone structure. For this purpose, segments of known proteins with a length of 3 and 5 amino acid residues are analyzed.