Maciej Maciejczyk

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A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result,(More)
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals(More)
A solution structure of the Ni(II) complex with the N-terminal pentadecapeptide of human protamine HP2 (HP2(1)(-)(15)) was elucidated with the use of a range of one- and two-dimensional (1)H NMR techniques and molecular modeling. A striking double-loop conformation was found, exhibiting the interactions of the aromatic ring of the Tyr(8) residue with the(More)
Glutathione disulfide (GSSG), a long disregarded redox partner of glutathione (GSH), is thought to participate in intracellular zinc homeostasis. We performed a concerted potentiometric and NMR spectroscopic study of protonation and Zn(II) binding properties of GSSG ((γECG)(2)) and a series of its nine analogs with C-terminal modifications, tripeptide(More)
GSH and L-His are abundant biomolecules and likely biological ligands for Zn(II) under certain conditions. Potentiometric titrations provide evidence of formation of ternary Zn(II) complexes with GSH and L-His or D-His with slight stereoselectivity in favour of L-His (ca. 1 log unit of stability constant). The solution structure of the ZnH(GSH)(L-His)(H2O)(More)
It is not certain whether the helix propagation parameters s(n)() (i.e., the equilibrium constants between (n - 1)- and n-residue long alpha-helices) determined from numerous studies of rather long model peptides are applicable for description of the initial steps of the helix formation during the protein folding process. From fluorescence, NMR, and(More)
Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3-5) interaction centers. van der Waals interactions are modeled by(More)
Modified mRNA cap analogs aid in the study of mRNA-related processes and may enable creation of novel therapeutic interventions. We report the synthesis and properties of 11 dinucleotide cap analogs bearing a single boranophosphate modification at either the α-, β- or γ-position of the 5',5'-triphosphate chain. The compounds can potentially serve either as(More)
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a(More)
Specific recognition and binding of the ribonucleic acid 5' termini (mRNA 5' cap) by the eukaryotic translation initiation factor 4E (eIF4E) is a key, rate limiting step in translation initiation. Contrary to mammalian and yeast eIF4Es that discriminate in favor of 7-methylguanosine cap, three out of five eIF4E isoforms from the nematode Caenorhabditis(More)