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1

The SAXS and Rheological Studies of HEWL Amyloid Formation

100%

Szymańska A., Ślósarek G., Hornowski T., Kozak M.

Acta Physica Polonica A

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2008

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vol. 114

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issue 2

447-454

EN

We performed small angle X-ray scattering and rheological experiments in order to analyze the aggregation and denaturation processes of hen egg white lysozyme initiated by the presence of ethanol molecule. At low ethanol concentrations (below 60% (v/v)) we did not observe any change of the radius of gyration of lysozyme and no drastic changes in viscosity of the protein solution. With the increase in ethanol concentration up to the final concentration of 85% (v/v) the viscosity of protein solution dramatically increased. For high ethanol concentration a pseudoplastic behavior of lysozyme solution was observed, indicating a process of aggregation and reorientation of the protein molecules. Similar effects were observed in small angle X-ray scattering experiments. We assume that the analysis of the aggregation processes of the hen egg white lysozyme could contribute to our understanding of the mechanism of lysozyme amyloid formation.

2

De Novo Designed Proteins - Perspective Materials for Nanotechnology

100%

Grzyb J.

Acta Physica Polonica A

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2012

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vol. 122

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issue 2

279-283

EN

The paper explores the field of de novo protein design, as a source of material for effective hybrid nanostructures. Main design approaches, namely the intuitional and the computational strategy, are briefly overviewed. The achievements in the field are illustrated with several examples, starting from historical heme binding maquettes to novel non-natural enzymes. Separate paragraph covers the problem of designing peptides, which may act as anchor between biological and non-biological parts of nanostructures. The advantages of de novo designed proteins and still existing problems of the field are discussed.

3

Investigation of Ferritin Desorption from Gold Initiated by In Situ pH-Change

80%

Poór V., Kasyutich O., Hallam K., Schwarzacher W.

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issue 2

394-396

EN

One of the main questions regarding protein adsorption is about the reversibility of the adsorption process. To get a deeper understanding of this, adsorption of ferritin on Au was studied by quartz crystal microbalance and the pH of the buffer was changed in situ between two values that favour adsorption by different amounts. We found that although some ferritin desorbs from Au, the desorption is incomplete. When the desorption reached a constant value, we returned to the original conditions and investigated the readsorption. Our experiments show that the adsorption of ferritin onto Au is a partly reversible process. We found that for different initial ferritin coverages the proportion of ferritin that had been subsequently desorbed was approximately constant.

4

Tests of the Structure-Based Models of Proteins

80%

Cieplak M., Sułkowska J.

Acta Physica Polonica A

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2009

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vol. 115

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issue 2

441-445

EN

The structure-based models of proteins are defined through the condition that their ground state coincides with the native structure of the proteins. There are many variants of such models and they yield different properties. Optimal variants can be selected by making comparisons to experimental data on single-molecule stretching. Here, we discuss the 15 best performing variants and focus on fine tuning the selection process by adjusting the velocity of stretching to match the experimental conditions. The very best variant is found to correspond to the 10-12 potential in the native contacts with the energies modulated by the Miyazawa-Jernigan statistical potential and variable length parameters. The second best model incorporates the Lennard-Jones potential with uniform amplitudes. We then make a detailed comparison of the two models in which theoretical surveys of stretching properties of 7510 proteins were made previously.

5

Plasmon Enhancement of Fluorescence in Single Light-Harvesting Complexes from em Amphidinium carterae

80%

Bujak Ł., Piątkowski D., Mackowski S., Wörmke S., Jung C., Bräuchle C., Agarwal A., Kotov N., Schulte T., Hofmann E., Brotosudarmo T., Scheer H., Govorov A., Hiller R.

Acta Physica Polonica A

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2009

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vol. 116

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issue S

S-22-S-25

EN

We show that single peridinin-chlorophyll a-protein light-harvesting complexes from dinoflagellate Amphidinium carterae placed near to silver nanoparticles show strongly enhanced fluorescence emission. Single molecule spectroscopy experiments performed at room temperature point toward an enhancement of more than an order of magnitude for optimal conditions. Irrespective of the enhancement, we observe no effect of the metal nanoparticle on the fluorescence emission energy of the complex. This result provides a way to control the optical properties of biomolecules via plasmon excitations in metal nanoparticles.

6

Low Resolution Structure of RAR1-GST-Tag Fusion Protein in Solution

80%

Taube M., Jarmołowski A., Kozak M.

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issue 2

307-310

EN

RAR1 is a protein required for resistance mediated by many R genes and function upstream of signaling pathways leading to H_{2}O_{2} accumulation. The structure and conformation of RAR1-GST-Tag fusion protein from barley (Hordeum vulgare) in solution was studied by the small angle scattering of synchrotron radiation. It was found that the dimer of RAR1-GST-Tag protein is characterized in solution by radius of gyration R_G = 6.19 nm and maximal intramolecular vector D_{max} = 23 nm. On the basis of the small angle scattering of synchrotron radiation SAXS data two bead models obtained by ab initio modeling are proposed. Both models show elongated conformations. We also concluded that molecules of fusion protein form dimers in solution via interaction of GST domains.

7

Comparative Analysis of KP-HSA Complex by Spectroscopic Methods

70%

Mąciażek-Jurczyk M., Równicka-Zubik J., Dyja R., Sułkowska A.

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EN

The main objective of the presented study was to characterize the high (HAS) and low affinity (LAS) binding sites of ketoprofen (KP) in human serum albumin (HSA) structure with the use of spectrofluorescence and proton nuclear magnetic resonance spectroscopy. In vitro fluorescence analysis was used to estimate the effect of KP on the HSA fluorescence. The association constants K_{a} [M^{-1}] of KP-HSA complex in the HAS were determined with the use of Scatchard, Klotz, and Hill analysis. The quenching K_{Q} [M^{-1}] constants were determined on the basis of the Stern-Volmer equation. Binding of ketoprofen to plasma protein was also studied with the use of 8-anilinonapthalene-1-sulfonic acid (ANS) and 5-dimethylaminonaphthalene-1-sulfonic acid (DNSA) as the fluorescence probes in IIIA and IIA subdomains of HSA, respectively. To estimate the cooperativeness in proteins Hill's coefficient n_{H} was used. The analysis of proton nuclear magnetic resonance spectra of KP in the presence of HSA allows us to observe the interactions between aromatic rings of the drug and the rings of amino acids located in the hydrophobic subdomains of the protein on the basis of the changes of chemical shifts Δ σ [ppm] of drug protons resonances. Moreover the K_{a} constants [M^{-1}] of KP-HSA complex in the LAS were determined.

8

From Atomic Resolution to Molecular Giants: an Overview οf Crystallographic Studies of Biological Macromolecules with Synchrotron Radiation

61%

Jaskolski M.

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issue 2

257-263

EN

Protein crystals have huge unit cells ( ≈100 Å) filled not only with ordered protein molecules but also in about 50% with liquid water. The phase problem in protein crystallography can be solved by molecular replacement (using a suitable model molecule), by isomorphous replacement (using heavy atom derivatives), or by multiwavelength anomalous difraction (using resonant scattering of synchrotron-generated X-rays by anomalous atoms, such as Se). X-ray diffraction by protein crystals produces thousands of reflections but since the models are very complex (many thousands of atoms), paucity of data is a serious problem and stereochemical restraints are necessary. In consequence, the highest possible resolution (minimum d-spacing in Bragg's Equation) should always be the experimental goal. Protein structures determined by crystallography are deposited in protein data bank, which currently holds more than 62000 entries. Recent methodological advancements, stimulated by a wide-spread use of powerful synchrotron sources and by structural genomics, have resulted in rapid acceleration of the structure elucidation process, and in addition help to obtain a better data. Protein crystallography has produced atomic models of gigantic macromolecular assemblies, including the ribosome. It is also providing accurate targets for structure-guided development of drugs.

9

Quantum Foundations of Resonant Recognition Model

61%

Keković G., Raković D., Tošić B., Davidović D., Cosić I.

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issue 5

756-759

EN

Biomolecular recognition is an open scientific problem, which has been investigated in many theoretical and experimental aspects. In that sense, there are encouraging results within Resonant Recognition Model (RRM), based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids in the primary structure of proteins and their biological activity. It has been found through an extensive research that proteins with the same biological function have a common frequency in their numerical spectra. This frequency was found then to be a characteristic feature for protein biological function or interaction The RRM model proposes that the selectivity of protein interactions is based on resonant energy transfer between interacting biomolecules and that this energy, electromagnetic in its nature, is in the frequency range of 10^{13} to 10^{15} Hz, which incorporates infra-red (IR), visible and a small portion of the ultra-violet (UV) radiation. In this paper, the quantum mechanical basis of the RRM model will be investigated using the solution in the simplified framework of Hückel-like theory of molecular orbits.

Refine search results

The SAXS and Rheological Studies of HEWL Amyloid Formation

De Novo Designed Proteins - Perspective Materials for Nanotechnology

Investigation of Ferritin Desorption from Gold Initiated by In Situ pH-Change

Tests of the Structure-Based Models of Proteins

Plasmon Enhancement of Fluorescence in Single Light-Harvesting Complexes from em Amphidinium carterae

Low Resolution Structure of RAR1-GST-Tag Fusion Protein in Solution

Comparative Analysis of KP-HSA Complex by Spectroscopic Methods

From Atomic Resolution to Molecular Giants: an Overview οf Crystallographic Studies of Biological Macromolecules with Synchrotron Radiation

Quantum Foundations of Resonant Recognition Model