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 Journal of Biomolecular NMR

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Insight into human insulin aggregation revisited using NMR derived translational diffusion parameters

Jerzy Sitkowski, Wojciech Bocian, Elżbieta Bednarek, Mateusz Urbańczyk, Wiktor Koźmiński, Piotr Borowicz, Grażyna Płucienniczak, Natalia Łukasiewicz, Iwona Sokołowska, Lech Kozerski


The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled 13C,15N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH parameter and the concentration on aggregation. The diffusion coefficient Dav was used for monitoring the overall average state of oligomeric ensemble in solution. The analysis of the experimental data of diffusion measurements, using the direct exponential curve resolution algorithm (DECRA) allows suggesting the two main components of the oligomeric ensemble. The 3D HSQC-iDOSY, (diffusion ordered HSQC) experiments performed on 13C, 15N-fully labeled insulin at the two pH values, 4 and 7.5, allow for the first time a more detailed experimental observation of individual components in the ensemble. The discussion involves earlier static and dynamic laser light scattering experiments and recent NMR derived translational diffusion results. The results bring new informations concerning the preparation of pharmaceutical formulation and in particular a role of Zn2+ ions. They also will enable better understanding and unifying the results of studies on insulin misfolding effects performed in solution by diverse physicochemical methods at different pH and concentration.

 

New Article in Methods

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High-dimensional NMR methods for intrinsically disordered proteins studies

Katarzyna Grudziąż, Anna Zawadzka-Kazimierczuk, Wiktor Koźmiński


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Intrinsically disordered proteins (IDPs) are getting more and more interest of the scientific community. Nuclear magnetic resonance (NMR) is often a technique of choice for these studies, as it provides atomic-resolution information on structure, dynamics and interactions of IDPs. Nonetheless, NMR spectra of IDPs are typically extraordinary crowded, comparing to those of structured proteins. To overcome this problem, high-dimensional NMR experiments can be used, which allow for a better peak separation. In the present review different aspects of such experiments are discussed, from data acquisition and processing to analysis, focusing on experiments for resonance assignment.

 

New Article in Journal of Biomolecular NMR

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Fast evaluation of protein dynamics from deficient 15N relaxation data

Łukasz Jaremko, Mariusz Jaremko, Andrzej Ejchart, Michał Nowakowski


https://media.springernature.com/original/springer-static/image/art%3A10.1007%2Fs10858-018-0176-3/MediaObjects/10858_2018_176_Fig3_HTML.gif

Simple and convenient method of protein dynamics evaluation from the insufficient experimental 15N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse 15N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N–H vectors on two different time scales, S2 and Rex, can be elucidated. The generalized order parameter, S2, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, Rex, identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.

 

Sympozjum sekcji NMR Polskiego Towarzystwa Chemicznego 2018

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Sympozjum sekcji Rezonansu Magnetycznego Polskiego Towarzystwa Chemicznego odbędzie się w dniach 19-20 kwietnia 2018, w Centrum Nauk Biologiczno-Chemicznych Uniwersytetu Warszawskiego.

 

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Czwartek

11.00 - 11.15 prof. dr hab. Wiktor Koźmiński Otwarcie
11.15 - 11.45 dr Tomasz Ratajczyk Wzmocnienie sygnału NMR biomolekuł metodą hiperpolaryzacji jądrowej indukowanej parawodorem
11.45 - 12.15 dr Igor Zhukow Badania struktury oraz dynamiki ludzkiego prionowego PrPC za pomocą spektroskopii NMR wysokiej zdolności rozdzielczej
12.15 - 12.45   Przerwa kawowa (sponsor: Bruker logo)
12.45 - 13.15 mgr Paweł Ołówek Najnowsze możliwości w dziedzinie spektrometrii NMR – JEOL
13.15 - 14.00 mgr Katarzyna Grudziąż Jak robić białka na NMR
14.00 - 15.40   Lunch (sponsor: Bruker logo)
15.30 - 15.50 mgr Maciej Kostrzewa Mechanochemiczne otrzymywanie solwatów i kokryształów Apremilastu stymulowane π-filowym rozpoznaniem molekularnym w ciele stałym
15.50 - 16.10 dr Tomasz Pawlak Badania dynamiki molekularnej za pomocą spektroskopii NMR w ciele stałym w steroidowych rotorach molekularnych
16.10 - 16.35 mgr Dariusz Gołowicz Swept Coherence Transfer - A New Approach to Quantitative 2D NMR
16.35 - ...   Relaks na Tarasie CNBCh (sponsor: LOGO)

Piątek

10.00 - 10.30 prof. dr hab. Jarosław Jaźwiński Związki kompleksowe rodu(II) z pochodnymi aminokwasów - nowe receptory ligandów organicznych
10.30 - 11.00 dr Witold Andrałojć Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by the GGU sequence at the 3’ terminus
11.00 - 11.30   Przerwa kawowa (sponsor: Bruker logo)
11.30 - 11.45 dr Katarzyna Trzeciak Wpływ stereochemii i chemicznej modyfikacji C-końca dermorfiny na oddziaływania peptyd fosfolipid
11.45 - 12.00 dr hab. Dariusz Pisklak Zastosowanie spektroskopii NMR w fazie stałej w badaniach stałych form leków
12.00 - 12.30 dr Beata Naumczuk Regioselektywność reakcji alkilowania modelowych nukleozydów przez pochodne SN38
12.30 - 14.15 dr Piotr Garbacz Magnetyczny rezonans jądrowy w polu elektrycznym
14.15 - 14.30 prof. dr hab. Wiktor Koźmiński Zamknięcie
14.30 - ...   Lunch (sponsor: Bruker logo)

 

 

 

 

New Article in International Journal of Biological Macromolecules

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Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

Michał Nowakowski, Łukasz Jaremko, Benedykt Wladyka, Grzegorz Dubin, Andrzej Ejchart, Paweł Mak


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BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues. In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns. Although the amino acid sequence of BacSp222 has no significant similarity to any known peptide or protein, a 3D structure similarity search indicates a close relation to other four-helix bundle-motif bacteriocins, such as aureocin A53, lacticin Q and enterocins 7A/7B. Assuming similar functions, biology, structure and physicochemical properties, we propose to distinguish the four-helix bundle bacteriocins as a new Type A in subclass IId of bacteriocins, containing linear, non-pediocin-like peptides.

 


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