Biological Molecular Machines

This book compares the mechanisms of mechano-chemical enzymes, cytoskeleton-dependent motors and molecular machines acting on DNA and other cell constituents. Most of them utilize the energy of nucleotide triphosphate hydrolysis to amplify kinetic events to give rise to relatively large conformational changes. However, the mechanistic paths of these machines are adapted to their specific cellular requirements. Molecular machines shape the cell, move intracellular cargo, sort their compartments and localize organelles within the cell, and defects in these sophisticated molecules may cause cellular defects and medical disabilities. Understanding the principles may lead to pharmacological and therapeutic applications. The book comprises three main parts: Part I introduces the necessary background in physical chemistry and molecular biophysics. The relevance of time scales of protein dynamics, chemical reactions, and diffusion are discussed. As transitions between intermediate states are relevant, a thorough introduction to kinetic concepts is given. Part II presents experimental approaches. At the most basal level, enzymatic ensemble assays are sufficient, but advanced methods use pre-steady state kinetics, or single-molecule experiments involving fluorescence resonance transfer, or laser trap assays giving insight to force-independent transitions. Part III discusses selected examples, specifically actin-dependent motors (Myosin II and V), microtubule-dependent motors and severing AAA ATPases (kinesin, dynein, spastin/katanin), DNA motors (RecBCD, SpoEIII, phi29) and large GTPases (atlastin).