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In the proposed book, the goal will be to present a range of examples for how the adoption of physical-chemical/statistical-mechanical concepts and techniques has allowed for precise physical insights to be obtained for the ribosome. While the text will focus on the ribosome, it is the editor’s expectation that this could serve as an introduction for physics-trained scientists (bachelor’s and higher) as they move into the study of other biological assemblies. To this end, the plan is to collect contributions from leaders in the field who have used physically grounded approaches to address this complex biomolecular assembly. This will include discussions of all aspects of ribosome function (assembly, catalysis, protein synthesis and machine-like dynamics). By covering this broad range of processes, the reader will be introduced to physical principles that guide dynamics in the ribosome.
In the proposed text, contributions from leading researchers will be invited, where the physical principles and questions will be described, as well as the current state of our understanding. In particular, the authors will focus how to characterize the energetics of a range of biologically relevant processes in the ribosome.
Key Feautres:
- Presents a range of examples for how the adoption of physical-chemical/statistical-mechanical concepts and techniques has allowed for precise physical insights to be obtained for the ribosome
- It will serve as an introduction for physics-trained scientists (bachelor’s and higher) as they move into the study of other biological assemblies
- Discussions will include all aspects of ribosome function (assembly, catalysis, protein synthesis and machine-like dynamics)
- Readers will be introduced to the physical principles that guide dynamics in the ribosome, as well as theoretical and experimental techniques that are suitable for further study.
- Proposed chapter authors (including two Nobel Laureates) are world class researchers in their respective fields.
Chapter 1: Energy Landscape Theory
Chapter 2: Dimensionality reduction methods
Chapter 3: Overview of Ribosome structure
Section 2: Ribosome Assembly
Chapter 4: The interface of theoretical and experimental probes of Assembly
Chapter 5: Quantifying the role of electrostatics during assembly of large RNA complexes
Section 3: Theoretical Methods for Chemical Reactions
Chapter 6: The mechanism of peptide bond formation
Chapter 7: Hydrolysis reactions and the dynamics of elongation factors
Section 4: Translation: Energetic determinants of kinetics and large-scale conformational processes
Chapter 8: Biochemical kinetic methods
Chapter 9: Single-molecule FRET methods
Chapter 10: Simplified energetic models and simulations
Chapter 11: The dynamics of elongation factors
Chapter 12: Time-resolved cryo-EM and manifold embedding
Chapter 13: Applications of atomistic simulations
Chapter 14: Using optical tweezers and fluorescence to probe translation kinetics
Section 5: Folding and release of nascent proteins on the ribosom
Chapter 15: Theoretical methods for folding on the ribosome
Chapter 16: The energetics of nascent chains
Chapter 17: Physical models for codon usage and fitness
Chapter 18: Optical tweezer approaches for studying nascent chain dynamics
Chapter 19: Modeling nascent protein release from the ribosome