Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Session IV Abstracts

What Was First, the Genetic Code or Its Products? Ada Yonath . Weizmann Institute of Science, Rehovot, Israel.

Ribosomes, the universal cellular machines for translation of the genetic code into proteins, possess spectacular architecture accompanied by inherent mobility, allowing for their smooth performance as polymerases that translate the genetic code into proteins. The site for peptide bond formation is located within a universal internal semi-symmetrical region. The high conservation of this region implies its existence irrespective of environmental conditions and indicates that it may represent an ancient RNA machine. Hence, it could be the kernel around which life originated. The mechanistic and genetic applications of this finding will be discussed.

The Photosynthetic Membrane of Purple Bacteria as a Clockwork of Atomic and Electronic Level Processes Klaus Schulten . University of Illinois at Urbana-Champaign, Urbana, IL, USA. The chromatophore of purple bacteria is a spherical bioenergetic membrane of 70 nm diameter with (by area) 90% protein content involving about 130 large protein complexes. With each chromatophore generated through invagination of the inner bacterial membrane, hundreds of chromatophores provide a bacterium with energy in the form of ATP, the synthesis of ATP being driven by sun light. The overall function in each chromatophore comes about through a clockwork of intertwined physical processes organized through a multi-million atom macromolecular structure. Recent progress has lead to a surprisingly rigorous description of key aspects of chromatophore biology: the huge overall structure got resolved down to its atomic, even electronic level, components; the physical mechanisms underlying the different participating processes have been largely identified and proven through computer simulations; the coupling of the different processes leading to a clockwork with robust and optimal photosynthetic function has been described in principle. This clockwork involves: (1) the quantum biological processes of light absorption, exciton formation, and coherent excitation transfer arising in so-called light harvesting proteins; (2) coupled electron-proton transfer and charging of the quinone-quinole pool achieved in a protein complex called the reaction center; (3) discharging of the quinone-quinole pool and charging of the membrane voltage achieved through electron-proton transfer realized in the bc1 protein complex; and (4) use of the membrane voltage by a protein complex called ATP synthase. The lecture exploits the most advanced molecular graphics achievable today (using the author's program VMD), and the most rigorous computational description of the subprocesses possible today (using the author's programs NAMD and PHI) offering views of the processes described as well as advanced and detailed computational (in particular also quantum chemical) descriptions.

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