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 Biological Inorganic Chemistry

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Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools

Chris A. E. M. Spronk, Szymon Żerko, Michał Górka, Wiktor Koźmiński, Benjamin Bardiaux, Barbara Zambelli, Francesco Musiani, Mario Piccioli, Priyanka Basak, Faith C. Blum, Ryan C. Johnson, Heidi Hu, D. Scott Merrell, Michael Maroney, Stefano Ciuri


HypA

Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3–7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.

 

New Article in The Journal of Physical Chemistry A

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Conformational Equilibrium of Cinchonidine in C6D12 Solution. Alternative NMR/DFT Approach

Sergey Molchanov, Tomasz Rowicki, Adam Gryff-Keller,  Wiktor Koźmiński


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1H NMR and 13C NMR chemical shifts as well as conformation dependent vicinal 1H–1H spin–spin coupling constants for cinchonidine in a dilute C6D12 solution have been measured. These data have been interpreted in detail exploiting the results of the extensive quantum chemistry calculations of molecular geometry and NMR parameters of the molecule, performed using the density functional theory (DFT) B3LYP/6-311++G(2d,p) polarizable continuum model (PCM) level of theory. The experimental values of NMR parameters for cinchonidine have been reproduced very well in terms of parameters calculated for key conformers of this molecule. Simultaneously, the analysis has provided us with a lot of information on conformational equilibrium of cinchonidine in the investigated solution. These findings remain in general agreement with the conclusions of other works, based on NOESY spectra or other physicochemical data. Thus, a careful quantitative interpretation of easily measurable NMR chemical shifts can be an independent and valuable source of structural information even in such complex cases as cinchonidine in solution.

 

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.

 

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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LOGO

 

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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


bakteriocyna

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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