Wiktor Koźmiński's NMR group

Biological and Chemical Research Centre, University of Warsaw

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Wiktor Koźmiński's NMR Group

Open Positions

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Project: New tools and applications of NMR spectroscopy beyond resolution limitation.

Project coordinator: prof. Wiktor Koźmiński.
Project duration: 2016 - 2021.

 

Positions for MSc students and Postdoc available.

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The aim of the project is an expansion of capabilities of the high-resolution nuclear magnetic resonance (NMR) spectroscopy which is a fundamental tool of modern structural biology. The structure and dynamics of proteins will be studied using new spectral parameters, such as cross-correlated relaxation rates. The research conducted in the frames of the project will make use of multidimensional NMR spectroscopy of isotopically enriched samples (13C, 15N, 2H) of proteins, both of folded and disordered nature. In addition, high hydrostatic pressure NMR will be employed to study conformational equilibria and dynamics of investigated proteins. Exceptionally high-resolution of 4 and 5 dimensional spectra will be achieved thanks to non-uniform sampling and advanced processing tools.

Candidate for MSc position shoud hold BSc preferably in chemistry, physics, biology or computer-science. All stipends are funded from NCN MAESTRO grant.

Postdoc candidates are asked to directly contact project coordinator.

More info: prof. Wiktor Koźmiński, This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Application deadline: ongoing recruitment.

 

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.

 

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 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.

 
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