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1

Przewidywanie struktury bialek: podejscie boltzmanowskie i darwinowskie

100%
Bujnicki J. M.
Kosmos
|
2005
|
tom 54
|
nr 2-3
155-162
2

A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide

100%
Bujnicki J. M.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 3-4
219-231
3

Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases

100%
Bujnicki J. M.
Acta Microbiologica Polonica
|
2000
|
tom 49
|
nr 1
4

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

100%
Bujnicki J. M.
Acta Biochimica Polonica
|
2001
|
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.
5

Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases

63%
Bujnicki J. M., Rychlewski L.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 1
6

Cloning and characterization of M.LmoA118I, a novel DNA: m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV

63%
Bujnicki J. M., Radlinska M.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 2
7

Cloning of enterohemorrhagic Escherichia coli phage VT-2 Dam methyltransferase

63%
Radlinska M., Bujnicki J. M.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 2
8

Prediction of a nowel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs

63%
Bujnicki J. M., Rychlewski L.
Acta Microbiologica Polonica
|
2000
|
tom 49
|
nr 3-4
9

Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV

63%
Radlinska M., Bujnicki J. M.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 2
10

Molecular phylogenetics of DNA 5mC-methyltransferases

63%
Bujnicki J. M., Radlinska M.
Acta Microbiologica Polonica
|
1999
|
tom 48
|
nr 1
11

Odgadywanie struktur życia

51%
Bujnicki J. M., Ginalski K., Kolinski A., Kosinski J.
Świat Nauki
|
2006
|
nr 02
12

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

51%
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.
13

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

51%
Radlinska M., Piekarowicz A., Galimand M., Bujnicki J. M.
Polish Journal of Microbiology
|
2005
|
tom 54
|
nr 3
A recent study revealed a subfamily of N6-adenine (m⁶A) methyltransferases that comprises a few functionally studied eukaryotic members acting on mRNA and prokaryotic members acting on DNA as well as numerous uncharacterized open reading frames. Here, we report cloning and functional characterization of a prokaryotic member of this family encoded by transposon Tn1549 from Enterococcus spp.
14

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

51%
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.
15
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Virtual screening strategies in drug design – methods and applications

39%
Bielska E., Lucas X., Czerwoniec A., Kasprzak J. M., Kaminska K. H., Bujnicki J. M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
|
2011
|
tom 92
|
nr 3
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