Biomedical subjects

Ivelitza Garcia

Publications and source records attributed to Ivelitza Garcia.

3 recordsLinked to original sources

PubMed2005

Resolution of three fluorescence components in the spectra of all-trans-1,6-diphenyl-1,3,5-hexatriene under isopolarizability conditions.

all-trans-1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence in solution consists of emissions from the S1 (2(1)A(g)) and S2 (1(1)B(u)) states of the s-trans,s-trans conformer (s-t-DPH) and emission from the S1 state of the s-cis,s-trans conformer (s-c-DPH). The contribution of s-c-DPH fluorescence increases upon excitation at longer wavelengths, and both minor emissions, s-c-DPH and 1(1)B(u) s-t-DPH fluorescence, contribute more at higher temperatures (Ts). Resolution of a spectrothermal matrix of DPH fluorescence spectra by principal component analysis with self-modeling (PCA-SM) is hampered by T-dependent changes in the spectra of the individual components. We avoided differential polarizability-dependent spectral shifts by measuring the spectra in n-alkanes (Cn, C8 to C16 with n even) at T values selected to keep the index of refraction constant, hence under isopolarizability conditions. Compensation of the spectra for T-induced broadening allowed resolution of the spectral matrix into its three components. The optimum van't Hoff plot gives Delta H = 2.83 kcal/mol for s-c-DPH/s-t-DPH equilibration, somewhat smaller than the 3.4 kcal/mol calculated value, and the optimum Boltzmann distribution law plot gives Delta E(ab) = 4.09 kcal/mol for 1(1)B(u)/2(1)A(g) equilibration. The 1(1)B(u) fluorescence spectrum bears mirror-image symmetry with the DPH absorption spectrum, and the energy gap, 1431 cm(-1), is consistent with the 1615 cm(-1) difference between the lowest energy bands in the 1(1)B(u) and 2(1)A(g) fluorescence spectra. The results give V(ab) = 198 +/- 12 cm(-1) for the vibronic matrix coupling element between the 2(1)A(g) and 1(1)B(u) states. Fluorescence quantum yields and lifetimes under isopolarizability conditions reveal an increase in the effective radiative rate constant of s-t-DPH with increasing T.

Journal Article↗

PubMed2004

Structural basis for the self-chaperoning function of an RNA collapsed state.

Prior to folding to a native functional structure, many large RNAs form conformationally collapsed states. Formation of the near-native collapsed state for the bI5 group I intron RNA plays an obligatory role in self-chaperoning assembly with its CBP2 protein cofactor by preventing formation of stable, misassembled complexes. We show that the collapsed state is essential because CBP2 assembles indiscriminately with the bI5 RNA in any folding state to form long-lived complexes. The most stable protein interaction site in the expanded state-CBP2 complex overlaps, but is not identical to, the native site. Folding to the collapsed state circumvents two distinct misassembly events: inhibitory binding by multiple equivalents of CBP2 and formation of bridged complexes in which CBP2 straddles cognate and noncognate RNAs. Strikingly, protein-bound sites in the expanded state RNA complex are almost the inverse of native RNA-RNA and RNA-protein interactions, indicating that folding to the collapsed state significantly reduces the fraction of RNA surfaces accessible for misassembly. The self-chaperoning function for the bI5 collapsed state is likely to be conserved in other ribonucleoproteins where a protein cofactor binds tightly at a simple RNA substructure or has an RNA binding surface composed of multiple functional sites.

Base Sequence↗

PubMed2003

Small structural costs for evolution from RNA to RNP-based catalysis.

Typical RNA-based cellular catalysts achieve their active structures only as complexes with protein cofactors, implying that protein binding compensates for some structural deficiencies in the RNA. An unresolved question was the extent to which protein-facilitation imposes additional structural costs, by requiring that an RNA maintain structures required for protein binding, beyond those required for catalysis. We used nucleotide analog interference to identify initially 71 functional group substitutions at phosphate, 2'-ribose, and adenosine base positions that compromise RNA self-splicing in the bI5 group I intron. Protein-facilitated splicing by CBP2 suppresses 11 of 30 interfering substitutions at the RNA backbone and a greater fraction, 27 of 41, at the adenosine base, including at structures conserved among group I introns. Only one substitution directly interferes with protein binding but not with self-splicing. This substitution, plus three adenosine base modifications that interfere more strongly in CBP2-dependent splicing than in self-splicing, yield a cost for protein facilitation of only four functional groups, as approximated by this set of analogs. The small observed structural cost provides a strong physical rationale for the evolutionary drive from RNA to RNP-based function in biology. Remarkably, the four extra requirements do not appear to report disruption of direct protein-RNA contacts and instead likely reflect design against misfolding rather than for maintenance of a protein-binding site.

Animals↗