Wyniki wyszukiwania

1

Helix-coil transition theories. Are they correct?

100%

Bierzynski A., Pawlowski K.

Acta Biochimica Polonica

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1997

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tom 44

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nr 3

Principles of contemporary theoretical description of a-helix formation by polypeptide chains in water solution are shortly presented and critically discussed. The theory treats the unfolded state of a peptide as "random coil" — an ideal conformation quite distant from reality. We suggest that for this reason the helix propagation parameters of amino-acid residues, determined using series of model peptides with different sequential patterns, are not the same. Interpretation of the so called "nucleation parameter" is erroneous. In fact, it is not determined by the helix nucleation process but rather by a specific situation of residues at the helix N- and C-termini, and it strongly depends on solvation of their NH and CO groups, respectively. Consequently, helical segments with terminal sequences dominated by residues with strongly hydrophobic, bulky side chains can be very unstable. We postulate that an unexpectedly high stability of very short, pre-nucleated helices studied by us arises from a "helix end separation effect": separated helix termini are better solvated than when they overlap each other. Because of this effect, helix initiation may be much more difficult than predicted by the theoretical "helix nucleation parameters".

2

Monte Carlo simulations of protein-like heteropolymers

100%

Sikorski A., Romiszowski P.

Acta Biochimica Polonica

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2001

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tom 48

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nr 1

Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hy- drophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.

3

On the possible methods for the mathematical description of the ball and chain model of ion channel inactivation

84%

Malysiak K., Grzywna Z. J.

Cellular and Molecular Biology Letters

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2008

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tom 13

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nr 4

535-552

Ion channels are large transmembrane proteins that are able to conduct small inorganic ions. They are characterized by high selectivity and the ability to gate, i.e. to modify their conductance in response to different stimuli. One of the types of gating follows the ball and chain model, according to which a part of the channel’s protein forms a ball connected with the intracellular side of the channel by a polypeptide chain. The ball is able to modify the conductance of the channel by properly binding to and plugging the channel pore. In this study, the polypeptide ball is treated as a Brownian particle, the movements of which are limited by the length of the chain. The probability density of the ball’s position is resolved by different diffusional operators — parabolic (including the case with drift), hyperbolic, and fractional. We show how those different approaches shed light on different aspects of the movement. We also comment on some features of the survival probabilities (which are ready to be compared with electrophysiological measurements) for issues based on the above operators.

4

Recycling of eucaryotic ribosomes

84%

Tyczewska A., Bakowska-Zywicka K.

Biotechnologia

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2009

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nr 1

81-85

5

Design of a knowledge-based force field for off-lattice simulations of protein structure

84%

Liwo A., Oldziej S., Kazmierkiewicz R., Groth M., Czaplewski C.

Acta Biochimica Polonica

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1997

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tom 44

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nr 3

Prediction of protein structure from amino-acid sequence still continues to be an unsolved problem of theoretical molecular biology. One approach to solve it is to construct an appropriate (free) energy function that recognizes the native structures of some selected proteins (whose native structures are known) as the ones distinctively lowest in (free) energy and then to carry out a search of the lowest-energy structure of a new protein. In order to reduce the complexity of the problem and the cost of energy evaluation, the so-called united-residue representation of the polypeptide chain is often applied, in which each amino-acid residue is represented by only a few interaction sites. Once the global energy minimum of the simplified chain has been found, the all-atom structure can easily and reliably be constructed. The search of the lowest-energy structure is usually carried out by means of Monte Carlo methods, though use of more efficient global-optimization methods, especially those of deformation of original energy surface is potentially promising. Monte Carlo search of the conformational space can be accelerated greatly, if the chain is superposed on a discrete lattice (the on-lattice approach). On the other hand, the on-lattice approach prohibits the use of many efficient global-optimization methods, because they require both energy and its space derivatives. The on-lattice methods in which the chain is embedded in the continuous 3D space are, therefore, also worth developing. In this paper we summarize the work on the design and implementation of an off-lattice united-residue force field that is underway in our group, in cooperation with Professor H.A. Scheraga of Cornell University, U.S.A.

6

Evidence for plant ribosomal 5S RNA involvement in elongation of polypeptide chain biosynthesis

84%

Shaikhin S., Sobkiewicz A., Barciszewski J., Twardowski T.

Acta Biochimica Polonica

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1994

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tom 41

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nr 1

A series of short oligo-DNA probes (8-10-mers) complementary to various regions of the plant ribosomal 5S ribonucleic acid (5S rRNA) have been synthesized. The results of their hybridization to free 5S rRNA and to ribosomes pointed to the availability of nucleotides in loop "C" for complexation. We found a correlation between hybridization of selected oligonucleotides and their inhibitory effect on enzymatic binding of Phe-tRNA and poly(Phe) synthesis on wheat germ 80S ribosomes. Evidence was obtained for involvement of 5S rRNA in the elongation of polypeptide chain during protein biosynthesis. 5S rRNA seems to play a critical role in protein biosynthesis, probably through causing conformational changes of loop C.

7

Computer simulations of protein folding with a small number of distance restraints

84%

Sikorski A., Kolinski A., Skolnick J.

Acta Biochimica Polonica

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2002

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tom 49

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nr 3

A high coordination lattice model was used to represent the protein chain. Lattice points correspond to amino-acid side groups. A complicated force field was designed in order to reproduce a protein-like behavior of the chain. Long-distance tertiary restraints were also introduced into the model. The Replica Exchange Monte Carlo method was applied to find the lowest energy states of the folded chain and to solve the problem of multiple minima. In this method, a set of replicas of the model chain was simulated independently in different temperatures with the exchanges of replicas allowed. The model chains, which consisted of up to 100 residues, were folded to structures whose root-mean-square deviation (RMSD) from their native state was between 2.5 and 5 A. Introduction of restrain based on the positions of the backbone hydrogen atoms led to an improvement in the number of successful simulation runs. A small improvement (about 0.5 A) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data.

8

Determination of single monosugars bound to a peptide

84%

Krotkiewski H., Krotkiewska B.

Acta Biochimica Polonica

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1997

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tom 44

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nr 2

A method is described which allows detection and quantitative determination of single monosugar units bound O-glycosidically to a peptide. A glycoprotein or a glycopeptide is chemically degraded under the modified conditions of Carlson degradation (beta-elimination performed in weakly alkaline conditions in the presence of sodium borohydride). An aliquot of the neutralized reaction mixture, supplemented with an internal standard, is peracetylated, extracted and directly analyzed by g.l.c.-m.s. All the O-linked oligosaccharides split off from the peptide are derivatized, but under gas-liquid chromatography at 150-230 degrees C only monosugar peracetylated alditols reach the detector. By comparing the retention times of appropriate peaks with standards and by checking their mass spectra the monosugar alditols are unequivocally identified. The detectable amount of a reduced monosugar in the analyzed sample is about 0.3 microgram. Several glycoproteins were analyzed using this method. Free N-acetylgalactosaminitol was detected in the degradation products of human glycophorin A and ovine submaxillary mucin, additionally free galactitol was detected in the degradation products of glycophorin. This result suggests that some single galactose units, O-glycosidically linked to the peptide are present in human glycophorin A.

9

Mouse monoclonal IgA antibodies lack interchain disulfide bonds

84%

Krotkiewski H., Laskowska A., Krotkiewska B.

Archivum Immunologiae et Therapiae Experimentalis

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1995

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tom 43

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nr 3-4

10

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3D domain swapping – implications for conformational disorders and ways of control

67%

Jaskolski M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2011

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tom 92

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nr 1

11

Similarity of vitamin D-binding protein (DBP) between various animal species in double immunodiffusion and western blotting

67%

Madej J. P., Boratynski J., Nowacki W.

Electronic Journal of Polish Agricultural Universities. Series Veterinary Medicine

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2007

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tom 10

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nr 3

12

Some parameters influencing immunoassay of human and horse myoglobins

67%

Kochanowska I. E., Kuropatwa M., Szewczuk A.

Archivum Immunologiae et Therapiae Experimentalis

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1997

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tom 45

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nr 2-3

Ograniczanie wyników

Helix-coil transition theories. Are they correct?

Monte Carlo simulations of protein-like heteropolymers

On the possible methods for the mathematical description of the ball and chain model of ion channel inactivation

Recycling of eucaryotic ribosomes

Design of a knowledge-based force field for off-lattice simulations of protein structure

Evidence for plant ribosomal 5S RNA involvement in elongation of polypeptide chain biosynthesis

Computer simulations of protein folding with a small number of distance restraints

Determination of single monosugars bound to a peptide

Mouse monoclonal IgA antibodies lack interchain disulfide bonds

3D domain swapping – implications for conformational disorders and ways of control

Similarity of vitamin D-binding protein (DBP) between various animal species in double immunodiffusion and western blotting

Some parameters influencing immunoassay of human and horse myoglobins