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Mariusz Jaskólski

Publications and source records attributed to Mariusz Jaskólski.

12 recordsLinked to original sources
PubMed2006

Checking the conformational stability of cystatin C and its L68Q variant by molecular dynamics studies: why is the L68Q variant amyloidogenic?

Human L68Q cystatin C is one of the known human amyloidogenic proteins. In its native state it is a monomer with alpha/beta structure. Experimental evidence suggests that L68Q variant associates into dimeric intermediates and that the dimers subsequently self-assemble to form amyloid deposits and insoluble fibrils. Details of the pathway of L68Q mutant amyloid formation are unclear; however, different experimental approaches with resolutions at molecular level have provided some clues. Probably, the stability and flexibility of monomeric L68Q variant play essential roles in the early steps of amyloid formation; thus, it is necessary to characterize early conformational changes of L68Q cystatin C monomers. In this paper, we demonstrate the possibility that the differences between the monomeric forms of wild-type (wt) cystatin C and its L68Q variant are responsible for higher tendency of the L68Q cystatin C amyloidogenesis. We started our studies with the simulations of wt and L68Q cystatin C monomers. Nanosecond time scale molecular dynamics simulations at 308K were performed using AMBER7.0 program. The results show that the structure of the L68Q monomer was changed, relative to the wt cystatin C structure. The results support earlier speculation that the L68Q point mutation would easily lead to dimer formation.

Amino Acid Substitution↗
PubMed2006

Molecular replacement with pseudosymmetry and model dissimilarity: a case study.

Crystals of human T-cell leukemia virus protease (HTLV-1 PR) have been very difficult to prepare and only native data extending to 2.6 angstroms resolution could be collected. Initial attempts to solve the structure with a variety of low-sequence-identity models utilizing proteases from other retroviruses and using a number of molecular-replacement programs were unsuccessful. The structure was finally solved using Phaser, revealing extensive pseudosymmetry and significant deviations from the starting models, features that were likely to be responsible for the initial failures. The steps taken to solve this structure and some of its intriguing crystallographic aspects are discussed.

Aspartic Acid Endopeptidases↗
PubMed2005

Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences.

S-Adenosylhomocysteine hydrolase (SahH) is involved in the degradation of the compound which inhibits methylation reactions. Using a Bayesian approach and other methods, we reconstructed a phylogenetic tree of amino acid sequences of this protein originating from all three major domains of living organisms. The SahH sequences formed two major branches: one composed mainly of Archaea and the other of eukaryotes and majority of bacteria, clearly contradicting the three-domain topology shown by small subunit rRNA gene. This topology suggests the occurrence of lateral transfer of this gene between the domains. Poor resolution of eukaryotes and bacteria excluded an ultimate conclusion in which out of the two domains this gene appeared first, however, the congruence of the secondary branches with SS rRNA and/or concatenated ribosomal protein datasets phylogenies suggested an "early" acquisition by some bacterial and eukaryotic phyla. Similarly, the branching pattern of Archaea reflected the phylogenies shown by SS rRNA and ribosomal proteins. SahH is widespread in Eucarya, albeit, due to reductive evolution, it is missing in the intracellular parasite Encephalitozoon cuniculi. On the other hand, the lack of affinity to the sequences from the alpha-Proteobacteria and cyanobacteria excludes a possibility of its acquisition in the course of mitochondrial or chloroplast endosymbioses. Unlike Archaea, most bacteria carry MTA/SAH nucleosidase, an enzyme involved also in metabolism of methylthioadenosine. However, the double function of MTA/SAH nucleosidase may be a barrier to ensure the efficient degradation of S-adenosylhomocysteine, specially when the intensity of methylation processes is high. This would explain the presence of S-adenosylhomocysteine hydrolase in the bacteria that have more complex metabolism. On the other hand, majority of obligate pathogenic bacteria due to simpler metabolism rely entirely on MTA/SAH nucleosidase. This could explain the observed phenetic pattern in which bacteria with larger (>6 Mb-million base pairs) genomes carry SAH hydrolase, whereas bacteria that have undergone reductive evolution usually carry MTA/SAH nucleosidase. This suggests that the presence or acquisition of S-adenosylhomocysteine hydrolase in bacteria may predispose towards higher metabolic, and in consequence, higher genomic complexity. The good examples are the phototrophic bacteria all of which carry this gene, however, the SahH phylogeny shows lack of congruence with SSU rRNA and photosyntethic genes, implying that the acquisition was independent and presumably preceded the acquisition of photosyntethic genes. The majority of cyanobacteria acquired this gene from Archaea, however, in some species the sahH gene was replaced by a copy from the beta- or gamma-Proteobacteria.

Adenosylhomocysteinase↗
PubMed2003

On the aromatic character of the heterocyclic bases of DNA and RNA.

Studies based on ab initio optimized geometries (at B3LYP/6-311+G** and MP2/6-311+G** levels) and on experimental structures retrieved from the Cambridge Structural Database (CSD) reveal that the nucleobases constituting DNA and RNA differ significantly in their aromatic character, as shown by the geometry-based index of aromaticity HOMA that ranges from 0.466 for thymine to 0.917 for adenine, based on B3LYP/6-311+G** calculations, and 0.495-0.926, respectively, if based on the MP2/6-311+G** level. Aromaticity of the bases decreases markedly with an increase of the number of double-bond C=X (X = N, O) substituents at the rings. H-bonds involving C=O groups in Watson-Crick pairs cause an increase of the aromatic character of the rings.

Adenine↗
PubMed2003

Hydrogen-bond networks in tris(4-hydroxyphenyl)methane and its 1:1 molecular complex with 4,4'-bipyridine.

In tris(4-hydroxyphenyl)methane (or 4,4',4"-methanetriyltriphenol), C(19)H(16)O(3), molecules are connected by O-H.O hydrogen bonds [O.O = 2.662 (2) and 2.648 (2) A] into two-dimensional square networks that are twofold interpenetrated. In tris(4-hydroxyphenyl)methane-4,4'-bipyridine (1/1), C(19)H(16)O(3).C(10)H(8)N(2), trisphenol molecules form rectangular networks via O-H.O [O.O = 2.694 (3) A] and C-H.O [C.O = 3.384 (3) A] hydrogen bonds. Bipyridine molecules hydrogen bonded to phenol moieties [O.N = 2.622 (3) and 2.764 (3) A] fill the voids to complete the structure.

Journal Article↗
PubMed2002

O-Benzyl-N-tert-butoxycarbonyl-N-methyl-L-tyrosine.

The crystal structure of the title compound, alternatively called 3-[4-(benzyloxy)phenyl]-2-(N-tert-butoxycarbonyl-N-methylamino)propionic acid, C(22)H(27)NO(5), has been studied in order to examine the role of N-methylation as a determinant of peptide conformation. The conformation of the tert-butoxycarbonyl group is trans-trans. The side chain has a folded conformation and the two phenyl rings are effectively perpendicular to one another. The carboxylate hydroxyl group and the urethane carbonyl group form a strong intermolecular O[bond]H...O hydrogen bond.

Journal Article↗
PubMed2002

Topological equivalences between organic and coordination polymer crystal structures: an organic ladder formed with three-connected molecular and supramolecular synthons.

[structure: see text] Crystal engineering of an organic ladder can be achieved with a T-shaped molecule, 4,4-bis(4'-hydroxyphenyl)-1-cyclohexanol, having three hydroxyl functionalities that can form O-H...O hydrogen-bonded helices. The topology of this network structure finds a parallel in three-connected coordination polymers.

Journal Article↗
PubMed2002

Prion diseases: a dual view of the prion hypothesis as seen from a distance.

We review the historical background and principles of the prion theory in its current shape. We showed that most of data may be still interpreted dually according to the protein only hypothesis and according to the theory in which additional component is necessary to comprise the infectivity. The enormous impact of structural biological studies is also stressed.

Animals↗
PubMed2001

Crystallization and preliminary crystallographic studies of five crystal forms of Escherichia coli L-asparaginase II (Asp90Glu mutant).

L-Asparaginase II from Escherichia coli with an Asp90Glu mutation in the active site has been crystallized in five polymorphic forms. Crystals of all polymorphs suitable for X-ray diffraction experiments were obtained by the vapour-diffusion method. Crystals of form I belong to the monoclinic system (space group C2), have unit-cell parameters a = 73.1, b = 133.1, c = 62.6 A, beta = 108.8 degrees and diffract to 2.27 A resolution. Three of the crystal forms are orthorhombic, with unit-cell parameters a = 225.4, b = 128.0, c = 62.6 A (form II, P2(1)2(1)2), a = 59.9, b = 71.2, c = 130.6 A (form III, primitive cell) and a = 73.8, b = 122.1, c = 124.2 A (form IV, P2(1)2(1)2(1) or P2(1)2(1)2); the crystals diffract to 2.33, 3.5 and 1.7 A, respectively. Polymorph V is trigonal, space group P3(1)21, with unit-cell parameters a = 123.1, c = 83.8 A; the crystals diffract to 2.65 A resolution.

Asparaginase↗