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M Illangasekare

Publications and source records attributed to M Illangasekare.

6 recordsLinked to original sources
PubMed1999

Specific, rapid synthesis of Phe-RNA by RNA.

RNA 77, derived by selection amplification, accelerates its own conversion to Phe-RNA (relative to randomized RNA) more than 6 x 10(7)-fold, by using amino acid adenylates as substrate. A modified assay system allows measurement of slow rates of aa-RNA formation, which for disfavored amino acid substrates can be more than 10(4)-fold slower than phenylalanine. Thus unlike previously characterized self-aminoacylators, RNA 77 catalysis is highly amino acid selective. Remarkably, both rates of aminoacyl transfer and amino acid specificities are greater for RNA 77 than measured for protein PheRS. These data experimentally support the possible existence of an ancestral amino acid-specific translation system relying entirely on RNA catalysis. RNA 77 itself embodies a possible transitional evolutionary state, in which side-chain-specific aa-RNA formation and anticodon-codon pairing were invested in the same molecule.

Acylation↗
PubMed1997

Essential structures of a self-aminoacylating RNA.

Comparison of six independent self-aminoacylating RNAs derived from selection-amplification, as well as deletion, addition, substitution, fragmentation of one particular RNA, are used to analyze the requirements for the RNA-catalyzed aminoacylation. All elements required for catalysis by one RNA family: sequence at the 3' acceptor end, calcium and magnesium sites, as well as the Phe-AMP substrate site and the essential 5' triphosphate terminus, are closely grouped near a bihelix junction in the parental molecule. All elements of the active center for aminoacyl transfer can therefore be captured by a peripherally-deleted helix junction RNA, defining a much smaller 43 nucleotide ribozyme, of which only 17 nucleotides were initially randomized. It appears that a complex RNA active center can be assembled by specifying unexpectedly few nucleotides, perhaps with a critical contribution from an essential calcium ion.

Acylation↗
PubMed1997

Small-molecule-substrate interactions with a self-aminoacylating ribozyme.

A self-aminoacylating RNA catalyst is shown to carry out the chemistry required for turnover, being reacylated several times from aminoacyl-AMP with an unaltered rate, thereby meeting one definition of an enzyme. Furthermore, a newly applied gel electrophoresis assay suggests first order kinetics in RNA and saturation kinetics in the substrate aminoacyl-adenylate, implying a Michaelis complex. AMP is a competitive inhibitor, though phenylalanine is not detectably inhibitory, consistent with a Michaelis complex through the AMP moiety of phenylalanyl-adenylate substrate. This idea is supported by measurement of elevated acylation velocities with seryl and alanyl-adenylates. The rate of aminoacylation increases with pH, consistent with attack of a terminal ribose oxyanion on the carbonyl carbon atom of the adenylate.

Acylation↗
PubMed1995

Aminoacyl-RNA synthesis catalyzed by an RNA.

An RNA has been selected that rapidly aminoacylates its 2'(3') terminus when provided with phenylalanyl-adenosine monophosphate. That is, the RNA accelerates the same aminoacyl group transfer catalyzed by protein aminoacyl-transfer RNA synthetases. The best characterized RNA reaction requires both Mg2+ and Ca2+. These results confirm a necessary prediction of the RNA world hypothesis and represent efficient RNA reaction (> or = 10(5) times accelerated) at a carbonyl carbon, exemplifying a little explored type of RNA catalysis.

Acylation↗
PubMed1988

Circular dichroism studies of distorted alpha-helices, twisted beta-sheets, and beta turns.

Theoretical models for calculating the circular dichroism (CD) of biopolymers have been constructed which allow the evaluation of the effects of geometric distortions within regular secondary structures. Outward tilting of the carbonyl group within alpha-helical structures yields calculated CD spectra with diminished intensity and a red-shifted maximum near 190 nm. The alpha II-helix provides an extreme example of this type of alpha-helix distortion. It is predicted that a mixture of alpha and alpha II structures in bacteriorhodopsin can account for its anomalous CD spectrum. The minimum length of alpha-helix required to produce an alpha-helix-like CD spectrum is calculated to be two to three turns (seven to eleven residues), while helices greater than 30 residues should provide adequate models of an infinite helix. Twisting of beta-sheets is predicted to lead to an increase in CD intensity and significant shifts in band position. Calculated CD spectra for beta-turn models are accurate for types II and II', but appear to be inadequate for type I turns.

Circular Dichroism↗