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Table of Contents
Preface; Contents; Part I: Introduction; Chapter 1: Biological Significance of Nascent Polypeptides That Stall the Ribosome; 1.1 Overview; 1.1.1 Importance of Nascent Peptidyl-tRNA in the ``Translation Concert ́ ́; 1.1.2 Nascent Polypeptides Can Modulate Progression of Their Own Translation; 1.1.3 Nascent Polypeptide-Mediated Translation Modulation Responds to Environmental Changes; 1.1.4 Regulatory Nascent Polypeptides Monitor and Control Cellular Physiology; 1.2 Concepts Characteristically Associated with Regulatory Nascent Polypeptides.
1.2.1 The Exit Tunnel Is Not Necessarily ``Teflon Like ́ ́1.2.2 Ribosomes Cannot Readily Synthesize Proteins Representing All the Possible Amino Acid Sequences; 1.2.3 The Use of a Posttranslational Determinant to Control Ongoing Translation; 1.2.4 Proteins Can Function Before They Are Completely Formed; 1.2.5 Nascent Polypeptides Can Direct the Subcellular Localization of mRNA; 1.2.6 Arrest Sequences Are Divergent in Their Primary Sequences; 1.2.7 Is Polypeptide-Directed Translational Pausing Ubiquitous?; 1.2.8 Arrest Control by the Dynamic Behavior of the Nascent Chain.
1.2.9 Quality Control Systems and Regulatory Nascent PolypeptidesReferences; Part II: The Ribosome and the Exit Tunnel; Chapter 2: Recent Progress in Ribosome Structure Studies; 2.1 Introduction; 2.2 Structure of the Ribosome; 2.3 Mechanism of Translation; 2.3.1 Initiation of Translation; 2.3.2 The Elongation Cycle; 2.3.3 Mechanism of Decoding: Preliminary Binding; 2.3.4 Mechanism of Decoding: Proofreading; 2.3.5 The Peptide Bond Formation; 2.3.6 Translocation; 2.3.7 Termination and Recycling; 2.3.8 Polypeptide Exit Tunnel; References.
Chapter 3: Structures of Nascent Polypeptide Chain-Dependent-Stalled Ribosome Complexes3.1 Introduction; 3.2 Cryo-EM Structure of the TnaC-SRC; 3.3 Cryo-EM Structure of the SecM-SRC; 3.4 Cryo-EM Structure of the CMV-SRC; 3.5 Cryo-EM Structure of the AAP-SRC; 3.6 Conclusions; References; Chapter 4: Tunnel Vision: Insights from Biochemical and Biophysical Studies; 4.1 Introduction; 4.2 The Physicochemical Properties of the Tunnel; 4.2.1 Tunnel Geometry; 4.2.2 Electrostatic Potentials in the Tunnel; 4.2.3 Effective Debye Length Along the Tunnel; 4.2.4 Water in the Tunnel; 4.2.5 pH in the Tunnel.
4.2.6 Solvent-Accessible Volume4.3 The Peptide in the Tunnel; 4.3.1 Side-Chain Chemistry: A Couple of Questions; 4.3.2 Peptide Folding in the Tunnel; 4.3.2.1 Compaction in the Tunnel; 4.3.2.2 Tertiary Folding in the Tunnel; 4.3.2.3 A Folding Vestibule in the Tunnel; 4.3.3 Peptide Movement Along the Tunnel; 4.3.4 Rearrangements in the Tunnel: Regional Discrimination and Pathway; 4.4 Movement of Tunnel Wall Components; 4.5 Peptide-Tunnel Interactions: Relay Mechanisms; 4.6 A New View Going Forward; References.
1.2.1 The Exit Tunnel Is Not Necessarily ``Teflon Like ́ ́1.2.2 Ribosomes Cannot Readily Synthesize Proteins Representing All the Possible Amino Acid Sequences; 1.2.3 The Use of a Posttranslational Determinant to Control Ongoing Translation; 1.2.4 Proteins Can Function Before They Are Completely Formed; 1.2.5 Nascent Polypeptides Can Direct the Subcellular Localization of mRNA; 1.2.6 Arrest Sequences Are Divergent in Their Primary Sequences; 1.2.7 Is Polypeptide-Directed Translational Pausing Ubiquitous?; 1.2.8 Arrest Control by the Dynamic Behavior of the Nascent Chain.
1.2.9 Quality Control Systems and Regulatory Nascent PolypeptidesReferences; Part II: The Ribosome and the Exit Tunnel; Chapter 2: Recent Progress in Ribosome Structure Studies; 2.1 Introduction; 2.2 Structure of the Ribosome; 2.3 Mechanism of Translation; 2.3.1 Initiation of Translation; 2.3.2 The Elongation Cycle; 2.3.3 Mechanism of Decoding: Preliminary Binding; 2.3.4 Mechanism of Decoding: Proofreading; 2.3.5 The Peptide Bond Formation; 2.3.6 Translocation; 2.3.7 Termination and Recycling; 2.3.8 Polypeptide Exit Tunnel; References.
Chapter 3: Structures of Nascent Polypeptide Chain-Dependent-Stalled Ribosome Complexes3.1 Introduction; 3.2 Cryo-EM Structure of the TnaC-SRC; 3.3 Cryo-EM Structure of the SecM-SRC; 3.4 Cryo-EM Structure of the CMV-SRC; 3.5 Cryo-EM Structure of the AAP-SRC; 3.6 Conclusions; References; Chapter 4: Tunnel Vision: Insights from Biochemical and Biophysical Studies; 4.1 Introduction; 4.2 The Physicochemical Properties of the Tunnel; 4.2.1 Tunnel Geometry; 4.2.2 Electrostatic Potentials in the Tunnel; 4.2.3 Effective Debye Length Along the Tunnel; 4.2.4 Water in the Tunnel; 4.2.5 pH in the Tunnel.
4.2.6 Solvent-Accessible Volume4.3 The Peptide in the Tunnel; 4.3.1 Side-Chain Chemistry: A Couple of Questions; 4.3.2 Peptide Folding in the Tunnel; 4.3.2.1 Compaction in the Tunnel; 4.3.2.2 Tertiary Folding in the Tunnel; 4.3.2.3 A Folding Vestibule in the Tunnel; 4.3.3 Peptide Movement Along the Tunnel; 4.3.4 Rearrangements in the Tunnel: Regional Discrimination and Pathway; 4.4 Movement of Tunnel Wall Components; 4.5 Peptide-Tunnel Interactions: Relay Mechanisms; 4.6 A New View Going Forward; References.