Wiktor Koźmiński's NMR group

Biological and Chemical Research Centre, University of Warsaw

  • Increase font size
  • Default font size
  • Decrease font size
Wiktor Koźmiński's NMR Group

Open Positions

Print

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.

alt

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 Chirality

Print

Size makes a difference: Chiral recognition in complexes of fenchone with cyclodextrins studied by means of NMR titration

Karolina Dudzik, Jacek Wójcik, Andrzej Ejchart, Michał Nowakowski


chirality MN

Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and naturally occurring cyclodextrins, βCD and γCD, were determined by means of 13C and 1H nuclear magnetic resonance (NMR) titration data. These results were compared with the corresponding data obtained previously for the diastereomeric fenchone/αCD complexes. The size of the inner cavity of host molecules significantly influences stoichiometry, association constants, and enantiomeric differentiation of the studied complexes. These complementary data allow us to discuss qualitatively the influence of the host size on the guest–host interactions. A method of the simultaneous use of titration data collected for several resonances of different isotopes in the determination of association constants was worked out and thoroughly analyzed. Comparison of the results of global data analyses with weighted means of individual ones revealed that both these approaches are equally trustworthy.

 

New Article in Frontiers in Microbiology

Print

Fast 2D NMR for in vivo Monitoring of Bacterial Metabolism in Complex Mixtures

Rupashree Dass, Katarzyna Grudziąż, Takao Ishikawa, Michał Nowakowski, Renata Dębowska, Krzysztof Kazimierczuk


fmicb 08 01306 g001

The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1H experiments have been reported in studies of bacterial metabolism monitored in situ. However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes, an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total “fingerprinting” of a sample and 2D 13C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

 

New Article in Journal of Biomolecular NMR

Print

Reconstruction of non-uniformly sampled five-dimensional NMR spectra by signal separation algorithm

Krzysztof Kosiński, Jan Stanek, Michał J. Górka, Szymon Żerko, Wiktor Koźmiński


cleaner5d

A method for five-dimensional spectral reconstruction of non-uniformly sampled NMR data sets is proposed. It is derived from the previously published signal separation algorithm, with major alterations to avoid unfeasible processing of an entire five-dimensional spectrum. The proposed method allows credible reconstruction of spectra from as little as a few hundred data points and enables sensitive resonance detection in experiments with a high dynamic range of peak intensities. The efficiency of the method is demonstrated on two high-resolution spectra for rapid sequential assignment of intrinsically disordered proteins, namely 5D HN(CA)CONH and 5D (HACA)CON(CO)CONH..

 

Congratulations!

Print

Congratulations to Saurabh Saxena on defending Ph.D. thesis entitled New NMR experiments for nucleic acids and intrinsically disordered proteins.

 

New Article in Journal of Biomolecular NMR

Print

Joint non-uniform sampling of all incremented time delays for quicker acquisition in protein relaxation studies

Mateusz Urbańczyk, Michał Nowakowski, Wiktor Koźmiński, Krzysztof Kazimierczuk


mateusz

NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of 15N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of 15N HSQC spectra can require several hours of measurement time. Standard non-uniform sampling (NUS), i.e. random under-sampling of indirect time domain, typically cannot reduce this by more than 2–4× due to relatively low “compressibility” of these spectra. In this paper we propose an extension of NUS to relaxation delays. The two-dimensional space of t1 /trelax is sampled in a way similar to NUS of t1/t2 domain in 3D spectra. The signal is also processed in a way similar to that known from 3D NUS spectra i.e. using one of the most popular compressed sensing algorithms, iterative soft thresholding. The 2D Fourier transform matrix is replaced with mixed inverse Laplace-Fourier transform matrix. The peak positions in resulting 3D spectrum are characterized by two frequency coordinates and relaxation rate and thus no additional fitting of exponential curves is required. The method is tested on three globular proteins, providing satisfactory results in a time corresponding to acquisition of two conventional 15N HSQC spectra.

 

New Article in Journal of the American Chemical Society

Print

Structure and Dynamics of the Huntingtin Exon-1 N-Terminus: A Solution NMR Perspective

Maria Baias, Pieter E. S. Smith, Koning Shen, Lukasz A. Joachimiak, Szymon Żerko, Wiktor Koźmiński, Judith Frydman, Lucio Frydman


htt

Many neurodegenerative diseases are characterized by misfolding and aggregation of an expanded polyglutamine tract (polyQ). Huntington’s Disease, caused by expansion of the polyQ tract in exon 1 of the Huntingtin protein (Htt), is associated with aggregation and neuronal toxicity. Despite recent structural progress in understanding the structures of amyloid fibrils, little is known about the solution states of Htt in general, and about molecular details of their transition from soluble to aggregation-prone conformations in particular. This is an important question, given the increasing realization that toxicity may reside in soluble conformers. This study presents an approach that combines NMR with computational methods to elucidate the structural conformations of Htt Exon 1 in solution. Of particular focus was Htt’s N17 domain sited N-terminal to the polyQ tract, which is key to enhancing aggregation and modulate Htt toxicity. Such in-depth structural study of Htt presents a number of unique challenges: the long homopolymeric polyQ tract contains nearly identical residues, exon 1 displays a high degree of conformational flexibility leading to a scaling of the NMR chemical shift dispersion, and a large portion of the backbone amide groups are solvent-exposed leading to fast hydrogen exchange and causing extensive line broadening. To deal with these problems, NMR assignment was achieved on a minimal Htt exon 1, comprising the N17 domain, a polyQ tract of 17 glutamines, and a short hexameric polyProline region that does not contribute to the spectrum. A pH titration method enhanced this polypeptide’s solubility and, with the aid of ≤5D NMR, permitted the full assignment of N17 and the entire polyQ tract. Structural predictions were then derived using the experimental chemical shifts of the Htt peptide at low and neutral pH, together with various different computational approaches. All these methods concurred in indicating that low-pH protonation stabilizes a soluble conformation where a helical region of N17 propagates into the polyQ region, while at neutral pH both N17 and the polyQ become largely unstructured—thereby suggesting a mechanism for how N17 regulates Htt aggregation.

 

New Article in Scientific Reports

Print

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

Tomasz Kochańczyk, Michał Nowakowski, Dominika Wojewska, Andrzej Ejchart, Wiktor Koźmiński, Artur Krężel


MichalZinkjpg

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.

 
  • «
  •  Start 
  •  Prev 
  •  1 
  •  2 
  •  3 
  •  4 
  •  5 
  •  Next 
  •  End 
  • »


Page 1 of 5






Banner
Banner
Banner

Conferences organized

by us:


 

euromar 2017 logo

 


 

mmcebanner3

 


 

AUM4

 


We use cookies to improve our website and your experience when using it. Cookies used for the essential operation of the site have already been set.

I accept cookies from this site.