Papers by Marta Pasenkiewicz-gierula
Journal of Magnetic Resonance (1969), 1986
Biochimie, 1991
Over the last half decade, we have studied saturated and unsaturated phosphatidylcholine (PC)-cho... more Over the last half decade, we have studied saturated and unsaturated phosphatidylcholine (PC)-cholesterol membranes, with special attention paid to fluid-phase immiscibility in cis-unsaturated PC-cholesterol membranes. The investigations were carried out with fatty acid and sterol analogue spin labels for which reorientational diffusion of the nitroxide was measured using conventional ESR technique. We also used saturation recovery ESR technique where dual probes were utilized. Bimolecular collision rates between a membrane-soluble square-planar copper complex,3-ethoxy-2-oxobutyraldehyde bis(N4,N4-dimethylthiosemicarbazonato)copper(II) (CuKTMS2) and one of several nitroxide radical lipid-type spin labels were determined by measuring the nitroxide spin-lattice relaxation time (TO. The results obtained in all these studies can be explained if the following model is assumed: 1) at physiological temperatures, fluid-phase micro-immiscibility takes place in cis-unsaturated PC-cholesterol membranes, which induces cholesterol-rich domains in the membrane due to the steric nonconformability between the rigid fused-ring structure of cholesterol and the 30 ° bend at the ci~ double bond of the alkyl chains of unsaturated PC. 2) The cholesterol-rich domains are small and/or of short lifetime (10-9 S tO < 10-.7 s). Our results also suggest that the extra space that is available for conformational disorder and accommodation of small molecules is created in the central part of the bilayer by intercalation of cholesterol in cis-unsaturated PC membrane due to the mismatch in the hydrophobic length and nonconformability between cis-unsaturated PC alkyl chains and the bulky tetracyclic ring of cholesterol. phospholipid unsaturation / cholesterol / phase separation / model membrane
Acta Biochimica Polonica, 1999
The main steps in the construction of a computer model for a bacterial membrane are described. Th... more The main steps in the construction of a computer model for a bacterial membrane are described. The membrane has been built of 72 lipid molecules, 54 of which being 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylethanolamine (POPE) and 18--1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidyl-rac-glycerol (POPG) molecules (thus in the proportion of 3:1). The membrane was hydrated with 1955 water molecules (approximately 27 water molecules per lipid). To neutralise the electronic charge (-e) on each POPG molecule, 18 sodium ions (Na+) were added to the membrane close to the POPG phosphate groups. The atomic charges on the POPE and POPG headgroups were obtained from ab initio quantum mechanical restrained electrostatic potential fitting (RESP) (Bayly et al., 1993, J. Phys. Chem. 97, 10269) using the GAMESS program at the 6-31G* level (Schmidt et al., 1993, J. Comput. Chem. 14, 1347). The model constructed in this way provided an initial structure for subsequent molecular dynamics simulation ...
Oxygen
Molecular oxygen (O2) is the perfect probe molecule for membrane studies carried out using the sa... more Molecular oxygen (O2) is the perfect probe molecule for membrane studies carried out using the saturation recovery EPR technique. O2 is a small, paramagnetic, hydrophobic enough molecule that easily partitions into a membrane’s different phases and domains. In membrane studies, the saturation recovery EPR method requires two paramagnetic probes: a lipid-analog nitroxide spin label and an oxygen molecule. The experimentally derived parameters of this method are the spin–lattice relaxation times (T1s) of spin labels and rates of bimolecular collisions between O2 and the nitroxide fragment. Thanks to the long T1 of lipid spin labels (from 1 to 10 µs), the approach is very sensitive to changes of the local (around the nitroxide fragment) O2 diffusion-concentration product. Small variations in the lipid packing affect O2 solubility and O2 diffusion, which can be detected by the shortening of T1 of spin labels. Using O2 as a probe molecule and a different lipid spin label inserted into sp...
Journal of Molecular Liquids, Sep 1, 2019
Monogalactosylodiacylglycerol (MGDG) is the main lipid component of thylakoid membranes. In water... more Monogalactosylodiacylglycerol (MGDG) is the main lipid component of thylakoid membranes. In water, MGDG molecules pack preferentially in the hexagonal H II phase, which consists of waterfilled lipid cylinders arranged in a hexagonal lattice. The H II phase can also form in the thylakoid membrane where it plays a key role in the photoprotection of the photosynthetic apparatus. In this study an all-atom computer model of the 16-cylinder MGDG H II phase was generated in a 3-μs molecular dynamics simulation and mathematical tools were developed to analyse its structural properties. The model-predicted values of the basic structural parameters, namely hexagonal spacing, circular and effective radii of the water channel, surface area/MGDG, and order parameters for the MGDG acyl chains, were compared with the experimental data available in the literature to validate the model. A stable computer model of the MGDG H II phase and the tools developed may serve further numerical experiments and investigations into the role of this phase in biological processes.
Postępy Biologii Komórki. Suplement, 2001
Postępy Biologii Komórki. Suplement, 2001
Acta Biochimica Polonica, Sep 30, 1997
Acta Biochimica Polonica, Sep 30, 1996
Current Eye Research, Sep 3, 2019
Purpose/Aim-The goal of this study is to reveal how age-related changes in phospholipid (PL) comp... more Purpose/Aim-The goal of this study is to reveal how age-related changes in phospholipid (PL) composition in the fiber cell plasma membranes of the human eye lens affect the cholesterol (Chol) content at which Chol bilayer domains (CBDs) and Chol crystals start to form. Materials and Methods-Saturation-recovery electron paramagnetic resonance with spinlabeled cholesterol analogs and differential scanning calorimetry were used to determine the Chol contents at which CBDs and cholesterol crystals, respectively, start to form in in membranes made of the major PL constituents of the plasma membrane of the human eye lens fiber cells. To preserve compositional homogeneity throughout the membrane suspension, the lipid multilamellar dispersions investigated in this work were prepared using a rapid solvent exchange method. The cholesterol content changed from 0 to 75 mol%. Results-The saturation recovery electron paramagnetic resonance results show that CBDs start to form at 33, 50, 46, and 48 mol% Chol in the phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and sphingomyelin bilayers, respectively. The differential scanning calorimetry results show that Chol crystals start to form at 50, 66, 70, and 66 mol% Chol in the phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and sphingomyelin bilayers, respectively. Conclusions-These results, as well those of our previous studies, indicate that the formation of CBDs precedes the formation of Chol crystals in all of the studied systems, and the appearance of each depends on the type of PL forming the bilayer. These findings contribute to a better understanding of the molecular mechanisms involved in the regulation of Chol-dependent processes in eye lens fiber cell membranes.
The Journal of Physical Chemistry, 1990
Copper(11) tetraphenylporphyrin, CuTPP, and di-spin-labeled copper(I1) hematoporphyrin IX, Cu-hem... more Copper(11) tetraphenylporphyrin, CuTPP, and di-spin-labeled copper(I1) hematoporphyrin IX, Cu-heme-SL2, are readily taken up into phospholipid bilayers of dimyristoylphosphatidylcholine, DMPC, and egg-yolk phosphatidylcholine, EYPC. Motional effects from the ESR data from both copper complexes are evident. These effects are parametrized in terms of a Cu-motion parameter, which is a measure of the degree of resolution of the nitrogen superhyperfine structure. Abrupt changes of the Cu-motion parameter at the main transition temperature of the DMPC bilayer demonstrate that hydrophobic copper complexes are sensitive probes of membrane fluidity. The nitrogen superhyperfine structure in the ESR spectra for CuTPP and Cu-heme-SL2 in light paraffin oil are particularly well resolved in the rigid-limit and fast-tumbling regions. The features of the ESR spectrum of CuTPP in DMPC liposomes are unusual and not attributed entirely to a rigid-limit or fast motion but to slow motion that needs further modeling.
Biochimie, Oct 1, 1991
Over the last half decade, we have studied saturated and unsaturated phosphatidylcholine (PC)-cho... more Over the last half decade, we have studied saturated and unsaturated phosphatidylcholine (PC)-cholesterol membranes, with special attention paid to fluid-phase immiscibility in cis-unsaturated PC-cholesterol membranes. The investigations were carried out with fatty acid and sterol analogue spin labels for which reorientational diffusion of the nitroxide was measured using conventional ESR technique. We also used saturation recovery ESR technique where dual probes were utilized. Bimolecular collision rates between a membrane-soluble square-planar copper complex,3-ethoxy-2-oxobutyraldehyde bis(N4,N4-dimethylthiosemicarbazonato)copper(II) (CuKTMS2) and one of several nitroxide radical lipid-type spin labels were determined by measuring the nitroxide spin-lattice relaxation time (TO. The results obtained in all these studies can be explained if the following model is assumed: 1) at physiological temperatures, fluid-phase micro-immiscibility takes place in cis-unsaturated PC-cholesterol membranes, which induces cholesterol-rich domains in the membrane due to the steric nonconformability between the rigid fused-ring structure of cholesterol and the 30 ° bend at the ci~ double bond of the alkyl chains of unsaturated PC. 2) The cholesterol-rich domains are small and/or of short lifetime (10-9 S tO < 10-.7 s). Our results also suggest that the extra space that is available for conformational disorder and accommodation of small molecules is created in the central part of the bilayer by intercalation of cholesterol in cis-unsaturated PC membrane due to the mismatch in the hydrophobic length and nonconformability between cis-unsaturated PC alkyl chains and the bulky tetracyclic ring of cholesterol. phospholipid unsaturation / cholesterol / phase separation / model membrane
TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk, 1998
Postępy Biologii Komórki. Suplement, 2001
Cellular & Molecular Biology Letters, 2005
Membrane proteins are essential constituents of the biological membranes. The lipid component of ... more Membrane proteins are essential constituents of the biological membranes. The lipid component of biomembranes, in the form of a bilayer, provides the basic physical barrier, whilst the membrane proteins regulate the permeability of this barrier to specific components and provide the membranous biological functions. Membrane proteins can be classified into two broad categories, integral and peripheral. Most biomembranes contain both types of membrane proteins. Integral membrane proteins have at least one segment that is embedded in the phospholipid bilayer. Transmembrane proteins span the entire phospholipid bilayer. The bilayer has two distinct regions, a polar interface and non-polar core. An integral protein contains mainly residues with hydrophobic side chains that interact with hydrocarbon chains of phospholipids in the membrane core but also residues with hydrophilic side chains that interact with polar headgroups of phospholipids at the membrane interface. These interactions anchor the protein to the membrane. The membrane-spanning domains are α helices or multiple β strands. Peripheral membrane proteins are entirely outside of the membrane, but are bound to it by weak molecular attractions. To elucidate the details of the protein-membrane interactions we adopted a strategy that involves studying the basic interactions of small peptides (~25 amino acids) with lipids in a bilayer of a lipid composition representative for the animal cell membrane. The study was carried out using molecular modelling methodology. We have chosen two computer models; one stands for the integral, the other for the peripheral membrane protein. In both systems, the animal cell membrane was modeled by a palmitoyloleoylphosphatidylcholine-cholesterol (POPC-Chol) bilayer. In the first model, the membrane spanning helical fragment of EGF receptor (EGF peptide) was inserted vertically to the bilayer surface, in the second, magainin-2 amide (M2a) was located on the bilayer surface [Murzyn, K. et al. Lect. Notes Comput. Sc. 3037 (2004) 325]. EGF receptor is a constitutive membrane protein, its transmembrane fragment consists mainly of hydrophobic amino acids. M2a is a natural cationic peptide expressed in the skin of a frog Xenopus leavis that selectively kills bacteria at concentrations that are harmless to animal cells. M2a consists of non-polar and charged (four positively charged Lys, N-terminus, and one negatively charged Glu) residues. In the membrane, M2a forms an α-helix of a distinct hydrophobic moment, i.e., the helix possesses a polar and non-polar face [Gesell, J. et al. J.
Oxygen, Aug 4, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Acta Biochimica Polonica, Mar 31, 2001
The structure of native a 1-antitrypsin, the most abundant protease inhibitor in human plasma, is... more The structure of native a 1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a b-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the b structure. The most common mutation in the protein, resulting in its inactivation, is Glu342®Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of a 1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of a 1-antitrypsin. u a reactive loop, exposed to solvent and containing the centre of proteinase inhibition (see Fig. 1),
Biochemical Journal, Jul 15, 1988
Although copper is quantitively removed from fungal laccase (Polyporus versicolor) by extended di... more Although copper is quantitively removed from fungal laccase (Polyporus versicolor) by extended dialysis against high concentrations of cyanide, we have been unable to reconstitute the protein by addition of Cu(I) ions. However, two new methods for reversibly removing the type 2 Cu centre have been developed. The visible absorption at 610 nm, which is attributable to type 1 Cu, is unaffected by the precedure, but the absorbance of the type 3 Cu at 330 nm is decreased by 60±10 O%. The decrease is due, at least in part, to partial reduction of the binuclear type 3 centre, although there may be some change in the molar absorptivity of the oxidized chromophore as well. The change in the c.d. spectrum that occurs at approx. 350 nm may be explained in the same way, but it may also reflect the loss of a signal due to the type 2 Cu. Upon removal of the type 2 Cu an absorbance increase appears at approx. 435 nm, and it is assigned to the semi-reduced form of the type 3 pair. In the e.p.r. spectrum of the type 2-depleted enzyme the type 1 Cu signal exhibits well-resolved ligand hyperfine splitting, which can be simulated on the basis of contributions from two N and two H nuclei (AH-AN-25 MHz). The H atoms are assumed to be attached to the ,-carbon of the covalently bonded cysteine ligand. A signal from a semi-reduced form(s) of the type 3 site can also be resolved in the spectrum of the type 2-depleted enzyme, and on the basis of the second integral of the e.p.r. spectrum 40 % of the type 3 pairs are believed to be in a partially reduced state. The semi-reduced type 3 site is remarkably stable and is not readily oxidized by H202 or IrCl62 or reduced by Fe(CN)64. Intramolecular electron transfer is apparently quite slow in at least some forms of the type 2-depleted enzyme, and this may explain why the activity is at best 5 % of that of the native enzyme. Full activity returns when type 2 copper is restored.
Biophysical Journal, Mar 1, 2000
A molecular dynamics (MD) simulation of a fully hydrated, liquid-crystalline dimyristoylphosphati... more A molecular dynamics (MD) simulation of a fully hydrated, liquid-crystalline dimyristoylphosphatidylcholine (DMPC)-Chol bilayer membrane containing ϳ22 mol% Chol was carried out for 4.3 ns. The bilayer reached thermal equilibrium after 2.3 ns of MD simulation. A 2.0-ns trajectory generated during 2.3-4.3 ns of MD simulation was used for analyses to determine the effects of Chol on the membrane/water interfacial region. In this region, 70% of Chol molecules are linked to DMPC molecules via short-distance interactions, where the Chol hydroxyl group (OH-Chol) is 1) charge paired to methyl groups of the DMPC choline moiety (ϳ34%), via the hydroxyl oxygen atom (Och); 2) water bridged to carbonyl (ϳ19%) and nonester phosphate (ϳ14%) oxygen atoms, via both Och and the hydroxyl hydrogen atom (Hch); and 3) directly hydrogen (H) bonded to carbonyl (ϳ11%) and nonester phosphate (ϳ5%) oxygen atoms, via Hch (ϳ17% of DMPC-Chol links are multiple). DMPC's ␥-chain carbonyl oxygen atom is involved in 44% of water bridges and 51% of direct H bonds formed between DMPC and Chol. On average, a Chol molecule forms 0.9 links with DMPC molecules, while a DMPC molecule forms 2.2 and 0.3 links with DMPC and Chol molecules, respectively. OH-Chol makes hydrogen bonds with 1.1 water molecules, preferentially via Hch. The average number of water molecules H bonded to the DMPC headgroup is increased by 7% in the presence of Chol. These results indicate that inclusion of Chol decreases interlipid links and increases hydration in the polar region of the membrane.
Uploads
Papers by Marta Pasenkiewicz-gierula