Electrostatics of nanosystems: Application to microtubules and the ribosome
TLDR
The application of numerical methods are presented to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size.Abstract:
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.read more
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References
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The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
TL;DR: The crystal structure of the large ribosomal subunit from Haloarcula marismortui is determined at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins.
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Classical Electrostatics in Biology and Chemistry
Barry Honig,Anthony Nicholls +1 more
TL;DR: A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the development of fast numerical and computational methods to solve the Poisson-Boltzmann equation for solute molecules that have complex shapes and charge distributions.
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The Structural Basis of Ribosome Activity in Peptide Bond Synthesis
TL;DR: It is established that the ribosome is a ribozyme and the catalytic properties of its all-RNA active site are addressed and the mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases.
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Structure of the 30S ribosomal subunit.
Brian T. Wimberly,Ditlev E. Brodersen,William M. Clemons,William M. Clemons,Robert J. Morgan-Warren,Andrew P. Carter,Clemens Vonrhein,Thomas Hartsch,Venki Ramakrishnan +8 more
TL;DR: The crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 Å resolution, is reported, which will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
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Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
Andrew P. Carter,William M. Clemons,William M. Clemons,Ditlev E. Brodersen,Robert J. Morgan-Warren,Brian T. Wimberly,Venki Ramakrishnan +6 more
TL;DR: The functional implications of the high-resolution 30S crystal structure are described, and details of the interactions between the 30S subunit and its tRNA and mRNA ligands are inferred, which lead to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.