9 items with the tag “rrna

  • Molecular Resurrection of the Ancestral Peptidyl Transferase Center
    NAI 2009 Georgia Institute of Technology Annual Report

    We have designed, and are resurrecting, a model of the a-PTC (ancestral Peptidyl Transferase Center), which we believe to be around 4 billion years old. The proposed a-PTC contains around 600 nucleotides of ancestral ribosomal RNA (a-rRNA), three ancestral ribosomal peptides (a-rPeptides), and inorganic cations, all of which are relatively straightforward to obtain or produce. The results of our molecular resurrection will allow one to test ideas about primitive living systems, including the origin of protein.

    ROADMAP OBJECTIVES: 3.2
  • RNA Folding and Assembly
    NAI 2009 Georgia Institute of Technology Annual Report

    We will characterize the assembly, structure and thermodynamics of the a-PTC by chemical mapping, including hydroxyl radical footprinting1,2 and SHAPE analysis,3 RNase H cleavage, temperature dependent hydrodynamics,4 and computational folding algorithms. In addition we will investigate the effect of freezing aqueous solutions of RNA and DNA molecules on their ability to assemble into larger more complex structures. Freezing nucleic acid solutions concentrates non-water molecules into small liquid pockets in the ice. This enables reactions that can promote the assembly of small segments of nucleic acids into larger complexes.

    ROADMAP OBJECTIVES: 3.2 5.3
  • High Level Theory - the Role of Mg2+ in Ribosome Assembly
    NAI 2009 Georgia Institute of Technology Annual Report

    We have embarked on a computational evaluation of the role of Mg2+ microclusters observed to form a scaffold for the extant and ancestral peptidyl transferase center. The interaction energies of ribosomal RNA with single and multiple Mg2+ cations are computed, and deconvolved. The results will be compared to those with other metals, to determine why Mg2+ plays a special role in RNA folding.

    ROADMAP OBJECTIVES: 3.2 5.3
  • Experimental Model System - an Ancestral Magnesium-RNA-Peptide Complex
    NAI 2009 Georgia Institute of Technology Annual Report

    We will develop small model systems in which the interactions of a-rPeptides, Mg2+ ions and a-rRNA can be studied by NMR, X-ray diffraction, calorimetry, molecular dynamics simulations, and other ‘high resolution’ biophysical techniques. Within the large subunit of the extant ribosome, one can observe a tail of ribosomal protein L2 (which we call a-rPeptideL2) that interacts with ribosomal helices rRNA 65 and 66 (which are conserved in a-rRNA), which in turn combines with Mg2+ to form a Mg2+-mc. We will define the smallest a-rRNA and peptide segments (of L2) that are sufficient for assembly of this complex and will characterize the assembly by a variety of experimental and computational methods.

    ROADMAP OBJECTIVES: 3.2
  • Molecular Resurrection of the Ancestral Peptidyl Transferase Center
    NAI 2010 Georgia Institute of Technology Annual Report

    We have resurrected, reconstructed, and are currently reconstituting a model of the a-PTC (ancestral Peptidyl Transferase Center), which we believe to have evolved around 4 billion years ago. The proposed a-PTC contains 644 nucleotides of ancestral ribosomal RNA (a-rRNA), five ancestral ribosomal peptides (a-rPeptides), and inorganic cations. Here we show data of the a-rRNA folding with Mg2+ and a-rPeptides

    ROADMAP OBJECTIVES: 3.2
  • High Level Theory - the Role of Mg2+ in Ribosome Assembly
    NAI 2010 Georgia Institute of Technology Annual Report

    We investigated a unique role of Mg2+ ions to form stable complexes with ribosomal RNA, and specifically their role in a formation of ancestral peptidyl transferase center using modern quantum mechanics methods. The interaction energies of ribosomal RNA with single and multiple Mg2+ cations are computed in the gas phase and water, and partitioned into specific tems. RNA-Mg interactions are compared to those with other metals, to determine why Mg2+ plays a special role in RNA folding. Additionally, we hypothesize a possible unique role of Fe2+ in a formation of ribosomal catalytic centers during early stages of life. The project is performed using NASA’s HEC supercomputer recourses.

    ROADMAP OBJECTIVES: 3.2 5.3
  • RNA Folding and Assembly
    NAI 2010 Georgia Institute of Technology Annual Report

    We will characterize the assembly, structure and thermodynamics of the a-PTC by chemical mapping, including hydroxyl radical footprinting1,2 and SHAPE analysis,3 RNase H cleavage, temperature dependent hydrodynamics,4 and computational folding algorithms. In addition we will investigate the effect of freezing aqueous solutions of RNA and DNA molecules on their ability to assemble into larger more complex structures. Freezing nucleic acid solutions concentrates non-water molecules into small liquid pockets in the ice. This enables reactions that can promote the assembly of small segments of nucleic acids into larger complexes.

    ROADMAP OBJECTIVES: 3.2 5.3
  • Experimental Model System - an Ancestral Magnesium-RNA-Peptide Complex
    NAI 2010 Georgia Institute of Technology Annual Report

    We are developing small model systems in which the interactions of rPeptides, Mg2+ ions and rRNA can be studied by NMR, X-ray diffraction, calorimetry, molecular dynamics simulations, and other ‘high resolution’ biophysical techniques. Within the large subunit of the extant ribosome, one observes an autonomous rRNA:Mg2+-mc complex in Domain III, which appears to fold independent of the rest of the LSU. Ribosomal protein L23 associates closely with this rRNA: Mg2+-mc complex in both bacteria and archaea, suggesting the possibility of distinct evolutionary origin. We will define the smallest Domain III rRNA and associated peptide segments sufficient for assembly of this complex, and will characterize their assembly and interactions with a-PTC and 23S lacking Domain III by a variety of experimental and computational methods.

    ROADMAP OBJECTIVES: 3.2