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Wyszukujesz frazę "Thermodynamics" wg kryterium: Temat

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    Wyświetlanie 1-6 z 6
    Tytuł:
    Elements of thermodynamics in RNA evolution.
    Autorzy:
    Kierzek, Elżbieta
    Biała, Ewa
    Kierzek, Ryszard
    Powiązania:
    https://bibliotekanauki.pl/articles/1044144.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    thermodynamics
    ribonucleic acids
    Opis:
    The paper presents some aspects correlating thermal stability of RNA folding and the occurrence of structural motifs in natural ribonucleic acids. Particularly, the thermodynamic stability of 2'-5' and 3'-5' linked RNA and the contribution of unpaired terminal nucleotides (dangling ends) in secondary (2D) and tertiary (3D) structures of RNA are discussed. Both examples suggest that during evolution nature selected sequences and structures of RNA which are the most thermally stable and efficient for their biological function.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 2; 485-493
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Thermodynamics of specific protein-RNA interactions.
    Autorzy:
    Stolarski, Ryszard
    Powiązania:
    https://bibliotekanauki.pl/articles/1043600.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    calorimetry
    thermodynamics
    fluorescence
    proteins
    specific binding
    RNA 5' cap
    Opis:
    Description of the recognition specificity between proteins and nucleic acids at the level of molecular interactions is one of the most challenging tasks in biophysics. It is key to understanding the course and control of gene expression and to the application of the thus acquired knowledge in chemotherapy. This review presents experimental results of thermodynamic studies and a discussion of the role of thermodynamics in formation and stability of functional protein-RNA complexes, with a special attention to the interactions involving mRNA 5' cap and cap-binding proteins in the initiation of protein biosynthesis in the eukaryotic cell. A theoretical framework for analysis of the thermodynamic parameters of protein-nucleic acid association is also briefly surveyed. Overshadowed by more spectacular achievements in structural studies, the thermodynamic investigations are of equal importance for full comprehension of biopolymers' activity in a quantitative way. In this regard, thermodynamics gives a direct insight into the energetic and entropic characteristics of complex macromolecular systems in their natural environment, aqueous solution, and thus complements the structural view derived from X-ray crystallography and multidimensional NMR. Further development of the thermodynamic approach toward interpretation of recognition and binding specificity in terms of molecular biophysics requires more profound contribution from statistical mechanics.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 2; 297-318
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data
    Autorzy:
    Maciejczyk, Maciej
    Hermans, Jan
    Bierzyński, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1041277.pdf
    Data publikacji:
    2006
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    thermodynamics
    peptide
    helix-coil equilibrium
    thermodynamic integration
    molecular dynamics
    Opis:
    Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid α-helix nucleus stabilized by La3+ coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.
    Źródło:
    Acta Biochimica Polonica; 2006, 53, 1; 121-130
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Interaction of anesthetic supplement thiopental with human serum albumin
    Autorzy:
    Khan, Shahper
    Islam, Barira
    Rajeswari, M
    Usmani,, Hammad
    Khan, Asad
    Powiązania:
    https://bibliotekanauki.pl/articles/1040762.pdf
    Data publikacji:
    2008
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    thiopental
    fluorescence resonance energy transfer
    thermodynamics
    FT-IR
    circular dichroism
    Opis:
    Thiopental (TPL) is a commonly used barbiturate anesthetic. Its binding with human serum albumin (HSA) was studied to explore the anesthetic-induced protein dysfunction. The basic binding interaction was studied by UV-absorption and fluorescence spectroscopy. An increase in the binding affinity (K) and in the number of binding sites (n) with the increasing albumin concentration was observed. The interaction was conformation-dependent and the highest for the F isomer of HSA, which implicates its slow elimination. The mode of binding was characterized using various thermodynamic parameters. Domain II of HSA was found to possess a high affinity binding site for TPL. The effect of micro-metal ions on the binding affinity was also investigated. The molecular distance, r, between donor (HSA) and acceptor (TPL) was estimated by fluorescence resonance energy transfer (FRET). Correlation between the stability of the TPL-N and TPL-F complexes and drug distribution is discussed. The structural changes in the protein investigated by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy reflect perturbation of the albumin molecule and provide an explanation for the heterogeneity of action of this anesthetic.
    Źródło:
    Acta Biochimica Polonica; 2008, 55, 2; 399-409
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Structure-function relationship of serine protease-protein inhibitor interaction.
    Autorzy:
    Otlewski, Jacek
    Jaskólski, Mariusz
    Buczek, Olga
    Cierpicki, Tomasz
    Czapińska, Honorata
    Krowarsch, Daniel
    Smalas, Arne
    Stachowiak, Damian
    Szpineta, Agnieszka
    Dadlez, Michał
    Powiązania:
    https://bibliotekanauki.pl/articles/1044133.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    calorimetry
    serine proteases
    structural thermodynamics
    protein inhibitor
    protein-protein recognition
    Opis:
    We report our progress in understanding the structure-function relationship of the interaction between protein inhibitors and several serine proteases. Recently, we have determined high resolution solution structures of two inhibitors Apis mellifera chymotrypsin inhibitor-1 (AMCI-I) and Linum usitatissimum trypsin inhibitor (LUTI) in the free state and an ultra high resolution X-ray structure of BPTI. All three inhibitors, despite totally different scaffolds, contain a solvent exposed loop of similar conformation which is highly complementary to the enzyme active site. Isothermal calorimetry data show that the interaction between wild type BPTI and chymotrypsin is entropy driven and that the enthalpy component opposes complex formation. Our research is focused on extensive mutagenesis of the four positions from the protease binding loop of BPTI: P1, P1', P3, and P4. We mutated these residues to different amino acids and the variants were characterized by determination of the association constants, stability parameters and crystal structures of protease-inhibitor complexes. Accommodation of the P1 residue in the S1 pocket of four proteases: chymotrypsin, trypsin, neutrophil elastase and cathepsin G was probed with 18 P1 variants. High resolution X-ray structures of ten complexes between bovine trypsin and P1 variants of BPTI have been determined and compared with the cognate P1 Lys side chain. Mutations of the wild type Ala16 (P1') to larger side chains always caused a drop of the association constant. According to the crystal structure of the Leu16 BPTI-trypsin complex, introduction of the larger residue at the P1' position leads to steric conflicts in the vicinity of the mutation. Finally, mutations at the P4 site allowed an improvement of the association with several serine proteases involved in blood clotting. Conversely, introduction of Ser, Val, and Phe in place of Gly12 (P4) had invariably a destabilizing effect on the complex with these proteases.
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 2; 419-428
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Mg 2+ Does not induce isomerization of the open transcription complex Escherichia coli RNA polymerase at the model Pα promoter bearing consensus -10 and -35 hexamers.
    Autorzy:
    Kolasa, Iwona
    Łoziński, Tomasz
    Wierzchowski, Kazimierz
    Powiązania:
    https://bibliotekanauki.pl/articles/1044041.pdf
    Data publikacji:
    2001
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    effect of Mg2+
    transcription open complex
    kinetics and thermodynamics of transcription initiation
    Opis:
    The kinetics and thermodynamics of the formation of the transcriptional open complex (RPo) by Escherichia coli RNA polymerase at the synthetic Pα promoter bearing consensus -10 and -35 recognition hexamers were studied in vitro. Previously, this promoter was used as a control one in studies on the effect of DNA bending by An·Tn sequences on transcription initiation and shown to be fully functional in E. coli (Łoziński et al., 1991, Nucleic Acids Res. 19, 2947; Łoziński & Wierzchowski, 1996, Acta Biochim. Polon. 43, 265). The data now obtained demonstrate that the mechanism of Pα-RPo formation and dissociation conforms to the three-step reaction model: bind-nucleate-melt, commonly accepted for natural promoters. Measurements of the dissociation rate constant of Pα -RPo as a function of MgCl2 concentration allowed us to determine the number of Mg2+ ions, nMg≈ 4, being bound to the RPo in the course of renaturation of the melted DNA region. This number was found constant in the temperature range of 25-37°C, which indicates that under these conditions the complex remaines fully open. This observation, taken together with the recent evidence from independent of the presence of Mg2+ ions (Łoziński & Wierzchowski, 2001, Acta KMnO4 footprinting studies that the length of the melted region in Pα-RPo at 37°C is Biochim. Polon. 48, 495), testifies that binding of Mg2+ to RPo does not induce its further isomerization, which has been postulated for the λPR-RPo complex (Suh et al., 1992, Biochemistry 31, 7815; 1993, Science 259, 358).
    Źródło:
    Acta Biochimica Polonica; 2001, 48, 4; 985-994
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-6 z 6

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