Wiktor Koźmiński's NMR group

Biological and Chemical Research Centre, University of Warsaw

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Wiktor Koźmiński's NMR Group

New Article in Biochemistry

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Impact of Calcium Binding and Thionylation of S100A1 Protein on Its Nuclear Magnetic Resonance-Derived Structure and Backbone Dynamics

Michał Nowakowski, Katarzyna Ruszczyńska-Bartnik, Monika Budzińska, Łukasz Jaremko, Mariusz Jaremko, Konrad Zdanowski, Andrzej Bierzyński, Andrzej Ejchart


 

S100 proteins play a crucial role in multiple important biological processes in vertebrate organisms acting predominantly as calcium signal transmitters. S100A1 is a typical representative of this family of proteins. After four Ca2+ ions bind, it undergoes a dramatic conformational change, resulting in exposure, in each of its two identical subunits, a large hydrophobic cleft that binds to target proteins. It has been shown that abnormal expression of S100A1 is strongly correlated with a number of severe human diseases: cardiomyopathy and neurodegenerative disorders. A few years ago, we found that thionylation of Cys 85, the unique cysteine in two identical S100A1 subunits, leads to a drastic increase of the affinity of the protein for calcium. We postulated that the protein activated by thionylation becomes a more efficient calcium signal transmitter. Therefore, we decided to undertake, using nuclear magnetic resonance methods, a comparative study of the structure and dynamics of native and thionylated human S100A1 in its apo and holo states. In this paper, we present the results obtained for both forms of this protein in its holo state and compare them with the previously published structure of native apo-S100. The main conclusion that we draw from these results is that the increased calcium binding affinity of S100A1 upon thionylation arises, most probably, from rearrangement of the hydrophobic core in its apo form.

 

New Article in Analytical Chemistry

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Iterative Thresholding Algorithm for Multiexponential Decay Applied to PGSE NMR Data

Mateusz Urbańczyk, Diana Bernin, Wiktor Koźmiński, Krzysztof Kazimierczuk


 

Pulsed gradient spin echo (PGSE) is a well-known NMR technique for determining diffusion coefficients. Various signal processing techniques have been introduced to solve the task, which is especially challenging when the decay is multiexponential with an unknown number of components. Here, we introduce a new method for the processing of such types of signals. Our approach modifies the Tikhonov’s regularization, known previously in CONTIN and Maximum Entropy (MaxEnt) methods, by using the -norm penalty function. The modification enforces sparsity of the result, which improves resolution, compared to both mentioned methods. We implemented the Iterative Thresholding Algorithm for Multiexponential Decay (ITAMeD), which employs the -norm minimization, using the Fast Iterative Shrinkage Thresholding Algorithm (FISTA). The proposed method is compared with the Levenberg–Marquardt-Fletcher fitting, Non-negative Least Squares (NNLS), CONTIN, and MaxEnt methods on simulated datasets, with regard to noise vulnerability and resolution. Also, the comparison with MaxEnt is presented for the experimental data of polyethylene glycol (PEG) polymer solutions and mixtures of these with various molecular weights (1080 g/mol, 11 840 g/mol, 124 700 g/mol). The results suggest that ITAMeD may be the method of choice for monodispersed samples with “discrete” distributions of diffusion coefficients.

 


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