(Macro)Molecular Crowding

This book offers a general overview of an important biological phenomenon known as macromolecular crowding. This phenomenon is rooted in the fact that the living cell contains very large quantities of various biological macromolecules, such as proteins, nucleic acids, and carbohydrates, whose concentration can be as high as 400 mg/ml, and which occupy about 30% of the cell volume. Such a crowded environment represents a type of cellular pottage with considerably restricted amounts of free water and has several specific characteristics, such as changing viscosity, water activity, and famous volume exclusion originating from the simple idea that the volume occupied by the cellular macromolecules is unavailable to other molecules. All this may have large effects on both stability of biological macromolecules and macromolecular equilibria, including proteinprotein interactions, protein folding, protein aggregation, and macromolecular association, as well as may lead to significant alterations in the rates of chemical reactions.

However, the effect of such a complex crowded environment on the behavior of biological macromolecules is poorly understood. This is because most of the biomolecular research in vitro is traditionally conducted in dilute solutions, which by no means can be considered adequate models of the extremely crowded intracellular space. To overcome these issues, multiple approaches are being developed to mimic macromolecular environments and to investigate biomolecules under these conditions of artificial crowding and confinement.

Importantly, recent years revealed that the distribution of macromolecules within the intracellular space is highly inhomogeneous; i.e., macromolecular crowding is characterized by the remarkable spatio-temporal heterogeneity, where one can find various membrane-less organelles and biological condensates representing overcrowded liquid droplets. The biogenesis of these highly dynamic cellular entities is driven by the liquid-liquid phase separation, and their formation typically represents a cellular response to the changing environment. These observations opened multiple new directions for a better understanding of the complexity and peculiarities of the cellular molecular kitchen.

This book aims at providing foundational information on these and related topics, which will be delivered by world-leading specialists in corresponding fields. By having chapters spread across all key foundational elements that come together in this field of study, this book will be the go-to reference in the area. It will provide guided access to the appropriate primary and secondary literature of this very exciting field. It also will provide a description of the physics of the process, give experimental guidance regarding the characterization of these phenomena, and show examples of well-understood systems. The book will provide a guide that will allow readers to rapidly form hypotheses and design experiments on their proteins or study system.

This book will help researchers to understand the relevant findings and help them to navigate through the clutter. Early career researchers as well as researchers coming from different fields need a basic reference to introduce them to this area and help them become productive and progress with their research faster.

Provides a comprehensive review of the rapidly expanding field of macromolecular crowding Covers a vast array of special topics and applications of molecular crowding in biology and biotechnology Includes in-depth discussions on various consequences of molecular crowding

Autorentext

Prof. Vladimir Uversky is a Professor at the Department of Molecular Medicine at the Morsani College of Medicine, University of South Florida (USF). He obtained Ph.D. from the Moscow Institute of Physics and Technology (1991) and a D.Sc. from the Institute of Experimental and Theoretical Biophysics (1998).

He obtained pre- and postdoctoral training in Structural Biology, Biochemistry, and Biophysics (1991-1998, Institute of Protein Research, Russian Academy of Sciences) and spent his early career working on protein folding at the Institute of Protein Research and the Institute for Biological Instrumentation (Russia). In 1998, he moved to the University of California Santa Cruz, where for six years he was studying protein folding, misfolding, protein conformation diseases, and protein intrinsic disorder phenomenon. In 2004, he was invited to join the Indiana University School of Medicine as a Senior Research Professor to work on intrinsically disordered proteins. Since 2010, he has been with USF, where he continues to study intrinsically disordered proteins, protein folding and misfolding processes, as well as liquid-liquid phase transitions and their applications in biology.

He has authored over 1500 scientific publications and edited several books and book series on protein structure, function, folding, and misfolding. Among his most recent edited volumes are "Droplets of Life: Membrane-less Organelles, Biomolecular Condensates, and Biological Liquid-Liquid Phase Separation" (ISBN: 9780128239674), "Structure and Intrinsic Disorder in Enzymology" (together with Munishwar Gupta, ISBN: 9780323995337), and The Three Functional States of Proteins: Structured, Intrin-sically Disordered, and Phase Separated (together with Prof. Timir Tripathi, ISBN: 9780443218095. He is also an editor of several scientific journals. In 2021, he was elected as a Fellow of the Royal Society of Biology and a Fellow of the Royal Society of Chemistry, and in 2024, he was elected as a Fellow of the American Institute for Medical and Biological Engineering and a Fellow of the American Association for the Advancement of Science.

Inhalt

Chapter 1: A brief historico-philosophical overview of macromolecular crowding: Making physiological conditions more physiological.- Chapter 2: Effects of molecular crowding on the structural, dynamic, and functional properties of biological macromolecules: A general overview.- Chapter 3: (Macro)molecular crowding effects beyond volume exclusion.- Chapter 4: Role of aqueous media in macromolecular crowding.- Chapter 5: Effects of macromolecular crowding on the structure and dynamics of biological membranes.- Chapter 6: Effects of molecular crowding on the structure, folding, and stability of DNA.- Chapter 7: Effects of molecular crowding on the structure, folding, stability, and catalysis of RNA.- Chapter 8: Understanding the effect of macromolecular crowding on protein misfolding and aggregation.- Chapter 9: The role of macromolecular crowding in cytoskeletal organization.- Chapter 10: Macromolecular crowding in cytoplasm and cellular organelles.- Chapter 11: Macromolecular crowding in mitochondria.- Chapter 12: Molecular crowing in nuclear pore.- Chapter 13: Catalytic Droplets: Enzyme Containing Microcompartments.- Chapter 14: Macromolecular crowding in cell stress and death.- Chapter 15: Heterogeneity of molecular crowding and liquid-liquid phase separation.- Chapter 16: Reshuffling overcrowded milieu: Stress-induced reorganization of the eukaryotic membrane-less organelles.- Chapter 17: Crowding in Anhydrobiosis.- Chapter 18: Crowding and in-cell crystallization.- Chapter 19: Macromolecular crowding for reparative medicine and drug discovery applications.- Chapter 20: Simulating crowding in vitro: Not an elusive goal any longer.- Chapter 21: Molecular Crowding by Computational Approaches.- Chapter 22: Modeling Facilitated Diffusion of Proteins in Crowded Environment.- Chapter 23: The Hidden Influences of Macromolecular Crowding: A New Frontier in Cellular Biology and Medicine.