Protoribosome by quantum kernel energy method

Abstract

Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the "protoribosome," which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory-B3LYP/3-21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome-namely (i) energetic structural stability and (ii) energetically stable attachment to substrates-are both well satisfied.bonding apparatus | puromycin | interaction energy | self-assembly | chemical model

Integrated evolution of ribosomal RNAs, introns, and intron nurseries

“…3, 4). For example, many introns are located within LSU rRNA domains II, IV, and V. These are among the earliest appearing sections of rRNA, which include the PTC, the P site, the A site, and the tunnel (Bokov and Steinberg 2009;Wekselman et al 2009;Belousoff et al 2010;Fox 2010;Huang et al 2013;Petrov et al 2014Petrov et al , 2015. Interestingly, only group I and group II introns occur in the PTC, which is suggestive of an ancient origin and rRNA association for these two classes of introns.…”

“…Introns have been found in the most ancient parts of rRNAs, suggesting primeval origins (Jackson et al 2002;Petrov et al 2014Petrov et al , 2015. This, together with reports that rRNAs were formed from the sequential addition of portions of rRNA during their early evolution, suggests that introns may have played a role in piecing together the functional sections of RNA that later became the rRNAs and, ultimately, ribosomes (Bokov and Steinberg 2009;Wekselman et al 2009;Belousoff et al 2010;Huang et al 2013;Petrov et al 2014Petrov et al , 2015.…”

“…From approximately 4.2-3.8 billion years ago, many innovative types of RNA evolved that played major roles in biology, during an era known as the "RNA world" (Darnell et al 1990;Alberts et al 1998;Gilbert et al 1997;Wekselman et al 2009;Belousoff et al 2010;Rogers 2017;Bada 2013;Huang et al 2013;Iwasa and Marshall 2016). This led to the assembly of the essential components of the central metabolic, evolutionary, and translational functions of ancient cells that still exist in modern cells (Darnell and Doolittle 1986;Gilbert et al 1997;Bujnicki and Rychlewski 2001;Roy et al 2002;Bokov and Steinberg 2009;Rogers 2017;Iwasa and Marshall 2016).…”

“…However, these early ribosomes also relied on the delivery of amino acids via tRNAs, which were charged by aminoacyl tRNA synthetases (protein enzymes), and short mRNAs. It is clear that, from very early in their evolution, ribosomes were (and still are) composed of complexes of structural, enzymatic, kinetic, and binding RNAs, as well as structural proteins (Bokov and Steinberg 2009;Fox 2010;Huang et al 2013;Petrov et al 2014Petrov et al , 2015Caetano-Annolés et al 2013;Caetano-Annolés and Caetano-Annolés 2015;Rogers 2017).…”

“…Recent studies indicate that sections of both the rRNA large subunit (LSU) and small subunit (SSU) predated the PTC of the LSU, and that the two subunits evolved separately prior to their association to form a protoribosome (Bokov and Steinberg 2009;Petrov et al 2014Petrov et al , 2015. For example, the PTC, tunnel, subunit association sites, P site (which holds the tRNA with the growing polypeptide), A site (which holds the tRNA with the incoming amino acid), and E site (where the exiting uncharged tRNA dissociates from the ribosome) were incorporated into rRNA at different times during early ribosome evolution, and complex decoding emerged only after all of these elements had been incorporated into the rRNA (Rodin and Rodin 2008;Bokov and Steinberg 2009;Wekselman et al 2009;Belousoff et al 2010;Fox 2010;Harish and Caetano-Anollés 2012;Caetano-Anollés et al 2013;Huang et al 2013;Petrov et al 2014Petrov et al , 2015Caetano-Anollés and Caetano-Anollés 2015). While the rRNA PTC appeared in one of the early phases of Petrov et al 2014Petrov et al , 2015, beginning more than 3.8 bya, are indicated for the evolution of AARSs (A, B), tRNA (C), mRNA (D), SSU rRNA (E), LSU rRNA (F).…”