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

100%
Bujnicki J. M.
|
2001
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vol. 48
|
issue 4
935-967
EN
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.
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Przewidywanie struktury białek: podejście boltzmannowskie i darwinowskie

100%
Bujnicki J. M.
Kosmos
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2005
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vol. 54
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issue 2-3
155-162
EN
Efforts to solve the problem of protein folding have been traditionally rooted in two schools of thought named Boltzmannian' and Darwinian', after the scientists who defined the fundamental principles of statistical thermodynamics and evolutionary biology, respectively. One approach to protein structure prediction is based on the principles of physics, e.g. on the thermodynamic hypothesis, according to which the native structure of a protein corresponds to the global minimum of its free energy under given conditions. Accordingly, the physics-based methods model the process of protein folding by simulating the conformational changes and searching for the free energy minimum. The other approach is based on the principles of evolution, in particular the empirical rule that evolutionarily related (homologous) proteins usually retain the same three-dimen-sional fold despite the accumulation of divergent mutations. Evolution-based methods attempt to map the sequence of the target protein to the structure of another protein (a template), model the overall fold of the target based on that of the template and infer how the target structures will change due to substitutions, insertions and deletions, as compared with the template. This review summarizes the basics of protein structure prediction by both types of approaches and discusses the issue of model quality evaluation.
3
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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., Radlińska M., Zaleski P., Piekarowicz A.
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2001
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vol. 48
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issue 4
969-983
EN
In this paper we report cloning and experimental characterization of the DNA adenine methyltransferase (dam) gene from Haemophilus influenzae and comparison of ts 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 tructural context. Both proteins share the common fold and essential cofactor-bind ng 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 rose by convergence.
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