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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.

SUBMITTER: Huang L

PROVIDER: S-EPMC3773780 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Protoribosome by quantum kernel energy method.

Huang Lulu L Krupkin Miri M Bashan Anat A Yonath Ada A Massa Lou L

Proceedings of the National Academy of Sciences of the United States of America 20130826 37

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 n ...[more]

PMID: 23980159

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Project description:Several simplifications used in clinical implementations of the convolution∕superposition (C∕S) method, specifically, density scaling of water kernels for heterogeneous media and use of a single polyenergetic kernel, lead to dose calculation inaccuracies. Although these weaknesses of the C∕S method are known, it is not well known which of these simplifications has the largest effect on dose calculation accuracy in clinical situations. The purpose of this study was to generate and characterize high-resolution, polyenergetic, and material-specific energy deposition kernels (EDKs), as well as to investigate the dosimetric impact of implementing spatially variant polyenergetic and material-specific kernels in a collapsed cone C∕S algorithm.High-resolution, monoenergetic water EDKs and various material-specific EDKs were simulated using the EGSnrc Monte Carlo code. Polyenergetic kernels, reflecting the primary spectrum of a clinical 6 MV photon beam at different locations in a water phantom, were calculated for different depths, field sizes, and off-axis distances. To investigate the dosimetric impact of implementing spatially variant polyenergetic kernels, depth dose curves in water were calculated using two different implementations of the collapsed cone C∕S method. The first method uses a single polyenergetic kernel, while the second method fully takes into account spectral changes in the convolution calculation. To investigate the dosimetric impact of implementing material-specific kernels, depth dose curves were calculated for a simplified titanium implant geometry using both a traditional C∕S implementation that performs density scaling of water kernels and a novel implementation using material-specific kernels.For our high-resolution kernels, we found good agreement with the Mackie et al. kernels, with some differences near the interaction site for low photon energies (<500 keV). For our spatially variant polyenergetic kernels, we found that depth was the most dominant factor affecting the pattern of energy deposition; however, the effects of field size and off-axis distance were not negligible. For the material-specific kernels, we found that as the density of the material increased, more energy was deposited laterally by charged particles, as opposed to in the forward direction. Thus, density scaling of water kernels becomes a worse approximation as the density and the effective atomic number of the material differ more from water. Implementation of spatially variant, polyenergetic kernels increased the percent depth dose value at 25 cm depth by 2.1%-5.8% depending on the field size, while implementation of titanium kernels gave 4.9% higher dose upstream of the metal cavity (i.e., higher backscatter dose) and 8.2% lower dose downstream of the cavity.Of the various kernel refinements investigated, inclusion of depth-dependent and metal-specific kernels into the C∕S method has the greatest potential to improve dose calculation accuracy. Implementation of spatially variant polyenergetic kernels resulted in a harder depth dose curve and thus has the potential to affect beam modeling parameters obtained in the commissioning process. For metal implants, the C∕S algorithms generally underestimate the dose upstream and overestimate the dose downstream of the implant. Implementation of a metal-specific kernel mitigated both of these errors.

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Protoribosome by quantum kernel energy method.

Publications

Protoribosome by quantum kernel energy method.

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