Wyniki wyszukiwania

1

Investigation of the applicability range of protein threading software

100%

Jaworski S., Sikorska C.

Current Topics in Biophysics. Supplement

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2011

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tom 34

|

nr A: Posters

2

Comparative analysis of HSV-1 temperature mutants proteins and their reactivity

100%

Litwinska B., Biesiadecka A., Gut W., Kantoch M.

Acta Microbiologica Polonica

|

1996

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tom 45

|

nr 2

3

MOFOID - not only the protein modelling server

88%

Szczesny P., Wieczorek G., Zielenkiewicz P.

Acta Biochimica Polonica

|

2005

|

tom 52

|

nr 1

MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user’s own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https://valis.ibb.waw.pl/mofoid/.

4

Beclin-1 and its role as a target for anticancer therapy

75%

Toton E., Lisiak N., Sawicka P., Rybczynska M.

Journal of Physiology and Pharmacology

|

2014

|

tom 65

|

nr 4

5

The structure of the synaptonemal complexes in meiocytes of European domestic goose [Anser anser]

75%

Andraszek K., Smalec E., Czyzewska D.

Folia Biologica

|

2008

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tom 56

|

nr 3-4

139-147

6

Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons

75%

Bujnicki J. M.

Acta Biochimica Polonica

|

2001

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tom 48

|

nr 4

Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.

7

Monte Carlo simulations of protein-like heteropolymers

75%

Sikorski A., Romiszowski P.

Acta Biochimica Polonica

|

2001

|

tom 48

|

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.

8

Artificially engineered specific nucleases - a breakthrough in RE research - Review

75%

Cesnaviciene E.

Biotechnologia

|

2003

|

nr 2

9

Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage

75%

Bujnicki J. M., Radlinska M., Zaleski P., Piekarowicz A.

Acta Biochimica Polonica

|

2001

|

tom 48

|

nr 4

In this paper we report cloning and experimental characterization of the DNA adenine methyltransferase (dam) gene from Haemophilus influenzae and comparison of its product with the Dam protein from the lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam and M.HP1Dam was carried out, providing a framework for a comparative analysis of these enzymes and their close homologs in the structural context. Both proteins share the common fold and essential cofactor-bind- ing and catalytic residues despite overall divergence. However, subtle but significant differences in the cofactor-binding pocket have been identified. Moreover, while M.HinDam seems to contact its target DNA sequence using a number of loops, most of them are missing from M.HP1Dam. Analysis of both MTases suggests that their catalytic activity was derived from a common ancestor, but similar sequence specificities arose by convergence.

10

AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family

63%

Pawlowski M., Lasica A. M., Jagusztyn-Krynicka E. K., Bujnicki J. M.

Polish Journal of Microbiology

|

2009

|

tom 58

|

nr 2

181-184

Dsb proteins control the formation and rearrangement of disulfide bonds during the folding of membrane and exported proteins. DsbA is an oxidant that catalyzes formation of disulfide bonds in newly synthesized, and yet unfolded proteins. In order to act catalytically again, it has to be reoxidized by a transmembrane protein DsbB characterized by two pairs of disulfides. DsbB is related to another protein family Dsbl, characterized by the presence of only one disulfide, and an additional C-terminal beta-propeller domain. The protein AAN82231 from E. coli strain CFT073 has been recently described as a new member of the Dsbl family (Grimshaw et al., 2008). It was found that AAN82231 forms a functional redox pair with DsbL - a newly described DsbA-like protein. Here, we report that AAN82231 shares no characteristic features with the Dsbl proteins. Instead, according to phylogenetic analyses AAN82231 clearly belongs to another, previously described subfamily of DsbB paralogs. To facilitate classification of DsbB and Dsbl homologs, we propose a new nomenclature system and present an updated phylogenetic analysis of the DsbB superfamily, which comprises the following families: "orthodox" DsbB, its paralogs now named DsbB2 (including AAN82231), Dsbl and two groups of so far uncharacterized DsbB paralogs termed DsbB3 and DsbB4. We have also developed a web server dedicated to phylogenetic assignment of DsbB/Dsbl candidate proteins that will be identified in the future.

11

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Novel roles for glutathione in linking oxidative stress to phytohormone-dependent signalling

63%

Noctor G., Han Y., Chaouch S., Mhamdi A.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

|

2013

|

tom 94

|

nr 2

12

A short review on proteomics and its applications

63%

Chandrasekhar K., Dileep A., Lebonah D. E., Pramoda Kumari J.

International Letters of Natural Sciences

|

2014

|

tom 12

|

nr 1

Proteomics is the large scale of study of proteins, particularly their function and structure. Proteomics is an excellent approach for studying changes in metabolism in response to different stress conditions. In the present review focused on different types of techniques for the analysis of expressed proteins. The techniques includes 2-D gel electrophoresis, MALDI-TOF/MS etc., play a vital role for the analysis of novel proteins and their role in disease maintenance and treatment. The review also concentrated on applicative perspective of proteomics in the fields of biomedical, agriculture and food.

13

Characterization and analyses of hydrophobic clusters, acetylation and myristoylation sites in plant glutathione peroxidase sequences

63%

Ganguli S., Polley A., Datta A.

International Letters of Natural Sciences

|

2015

|

tom 01

Incomplete reduction of oxygen molecules is the primary source for the formation of reactive oxygen species (ROS) during cytosolic metabolism or mitochondrial respiration. These phenomenons may be as a result of biotic or abiotic stress. Exposure to exogenous stimuli such as radiation might be an alternative pathway of ROS production. Thus plants require counter defense strategies to combat the increase of this toxic molecular build up in its cell cytoplasm. As a result they have devised an army of free radical scavenging enzymes which enable them to dissipate the oxidative stress imposed by the accumulation of these toxic moieties. Glutathione Peroxidase forms an important part of this arms race along with several catalases and organelle specific enzymes such as superoxide dismutase. Plant glutathione peroxidases(GPXs) have been studied exclusively for their evolutionary lineages since they represent a hybrid class of molecules in context of the presence and absence of selenocysteine at their catalytic centres, the former situation predominant in non vascular plant groups while the later a predominant feature of vascular plants. This analysis focuses on three important aspects of protein structure analyses – hydrophobic cluster analyses for identification of homologues, and acetylation and myristoylation sites which provide us with information regarding the post translational modifications of a particular protein group. Specific patterns of clusters along with acetylation and myristoylation site frequencies were obtained which indicate that GPXs of non vascular plant members possess less chances of getting myristoylated while acetylation was predominant in most land plant lineages but absent in aquatic members.

14

Denatured proteins and early folding intermediates simulated in a reduced conformational space

63%

Kmiecik S., Kurcinski M., Rutkowska A., Gront D., Kolinski A.

Acta Biochimica Polonica

|

2006

|

tom 53

|

nr 1

Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.

15

Comparison of proteins based on segments structural similarity

63%

Plewczynski D., Pas J., Von Grotthuss M., Rychlewski L.

Acta Biochimica Polonica

|

2004

|

tom 51

|

nr 1

We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Ca chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity measure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolShop structure prediction evaluation program and shows that our tool is on average slightly less sensitive than the DALI server. Both algorithms give a similar number of correct models, however, the final alignment quality is better in the case of DALI. Our method was implemented under the name 3D-Hit as a web server at http://3dhit.bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences.

16

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

63%

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

Acta Biochimica Polonica

|

1997

|

tom 44

|

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.

17

High coordination lattice models of protein structure, dynamics and thermodynamics

63%

Kolinski A., Skolnick J.

Acta Biochimica Polonica

|

1997

|

tom 44

|

nr 3

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force Held, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.

18

The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling medhods

63%

Jezierski G., Pasenkiewicz-Gierula M.

Acta Biochimica Polonica

|

2001

|

tom 48

|

nr 1

The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and aβ-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 β 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 α1-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 α1-antitrypsin.

19

Directionality of kinesin motors

63%

Kasprzak A. A., Hajdo L.

Acta Biochimica Polonica

|

2002

|

tom 49

|

nr 4

Kinesins are molecular motors that transport various cargoes along microtubule tracks using energy derived from ATP hydrolysis. Although the motor domains of kinesins are structurally similar, the family contains members that move on microtubules in opposite directions. Recent biochemical and biophysical studies of several kinesins make it possible to identify structural elements responsible for the different directionality, suggesting that reversal of the motor movement can be achieved through small, local changes in the protein structure.

20

Ciliate mating types and their specific protein pheromones

63%

Luporini P., Alimenti C., Ortenzi C., Vallesi A.

Acta Protozoologica

|

2005

|

tom 44

|

nr 2

Ograniczanie wyników

Investigation of the applicability range of protein threading software

Comparative analysis of HSV-1 temperature mutants proteins and their reactivity

MOFOID - not only the protein modelling server

Beclin-1 and its role as a target for anticancer therapy

The structure of the synaptonemal complexes in meiocytes of European domestic goose [Anser anser]

Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons

Monte Carlo simulations of protein-like heteropolymers

Artificially engineered specific nucleases - a breakthrough in RE research - Review

Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage

AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family

Novel roles for glutathione in linking oxidative stress to phytohormone-dependent signalling

A short review on proteomics and its applications

Characterization and analyses of hydrophobic clusters, acetylation and myristoylation sites in plant glutathione peroxidase sequences

Denatured proteins and early folding intermediates simulated in a reduced conformational space

Comparison of proteins based on segments structural similarity

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

High coordination lattice models of protein structure, dynamics and thermodynamics

The effect of the Glu342Lys mutation in alpha1-antitrypsin on its structure, studied by molecular modelling medhods

Directionality of kinesin motors

Ciliate mating types and their specific protein pheromones