Microcompartmentation and Phase Separation in Cytoplasm -

Microcompartmentation and Phase Separation in Cytoplasm (eBook)

A Survey of Cell Biology
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1999 | 1. Auflage
352 Seiten
Elsevier Science (Verlag)
978-0-08-085731-2 (ISBN)
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International Review of Cytology presents current advances and comprehensive reviews in cell biology-both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Authored by some of the foremost scientists in the field, each volume provides up-to-date information and directions for future research.This volume provides an overview of major cytoplasmic properties and events which including cytoarchitecture and the physical properties of cytoplasm, molecular compartmentation and gradients, channeling, sorting, and trafficking. It also addresses physicochemical events, both measured and anticipated, which attend solutions under conditions prevailing in cytoplasm: molecular crowding. It summarizes the current state of knowledge in the field and considers questions such as how molecules in cytoplasm interact.
International Review of Cytology presents current advances and comprehensive reviews in cell biology-both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Authored by some of the foremost scientists in the field, each volume provides up-to-date information and directions for future research.This volume provides an overview of major cytoplasmic properties and events which including cytoarchitecture and the physical properties of cytoplasm, molecular compartmentation and gradients, channeling, sorting, and trafficking. It also addresses physicochemical events, both measured and anticipated, which attend solutions under conditions prevailing in cytoplasm: molecular crowding. It summarizes the current state of knowledge in the field and considers questions such as how molecules in cytoplasm interact.

Front Cover 1
Microcompartmentation and Phase Separation in Cytoplasm 4
Copyright Page 5
CONTENTS 8
Contributors 14
Preface 16
PART I: PHYSICOCHEMICAL PROPERTIES OF AQUEOUS PHASE SYSTEMS AND PARTITIONING BEHAVIOR OF BIOMATERIALS 18
Chapter 1. Compositions and Phase Diagrams for Aqueous Systems Based on Proteins and Polysaccharides 20
I. Introduction: Limited Compatibility of Macromolecular Compounds 20
II. Phase Diagrams 24
III. Factors Affecting Phase Behavior of Biopolymer Mixtures 31
IV. Features of the Composition-Property Relationships in Mixed Biopolymer Systems 39
V. Concluding Remarks 43
References 44
Chapter 2. Partitioning and Concentrating Biomaterials in Aqueous Phase Systems 50
I. Introduction 50
II. Aqueous Phase Systems 52
III. Partitioning of Biomaterials 58
IV. Concentration of Proteins 72
V. Concluding Remarks 73
References 74
Chapter 3. Effects of Specific Binding Reactions on the Partitioning Behavior of Biomaterials 78
I . Introduction 78
II. Theoretical Considerations of Affinity Partitioning 80
III. Selection of Ligands and Mode of Coupling 84
IV. Affinity Partitioning of Proteins 88
V. Partitioning of Genetically Engineered Proteins 94
VI. Factors influencing Affinity Partitioning of Proteins 94
VII. Affinity Partitioning of Cell Membranes and Cells 99
VIII. Affinity Partitioning of Nucleic Acids 104
IX. Concluding Remarks 105
References 108
Chapter 4. Properties of Interfaces and Transport across Them 116
I. Introduction 116
II. Interfaces 117
III. Properties of Interfaces and Phases 128
IV. Equilibrium Partitioning across Interfaces 136
V. Transport across Interfaces 141
VI. The Time Scale for Phase Formation 148
VII. Summary 149
References 151
Chapter 5. Compartmentalization of Enzymes and Distribution of Products in Aqueous Two-Phase Systems 154
I. Introduction 154
II. Thermodynamic Forces for Partitioning of Proteins and Solutes between Two Aqueous Polymer Phases 156
III. Enzyme Reactions in Aqueous Phase Systems 161
IV. Concluding Remarks 167
References 168
PART II: PHYSICOCHEMICAL PROPERTIES OF CYTOPLASM 170
Chapter 6. Macromolecular Crowding and Its Consequences 172
I. Introduction: Phase Separation in Macromolecular Solutions 172
II. Macromolecular Crowding 175
III. Flory-Huggins Theory 176
IV. The Potential for Liquid–Liquid Phase Separation in the Cytosol: A Flory-Huggins Model 178
V. Conclusion 186
References 186
Chapter 7. Lens Cytoplasmic Phase Separation 188
I. Introduction 188
II. Development of Transparency 189
III. Phase Separation and Lens Cytoplasmic Proteins 190
IV. Phase Diagrams for Lens Cytoplasmic Proteins 192
V. Effects of Composition on the Phase Diagram 193
VI. Endogenous Mechanisms for Regulation of Phase Separation 197
VII. Phase Separation and Cellular Stnrctures 199
VIII. Concluding Remarks 201
References 201
Chapter 8. Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, lntracellular Surface Area 206
I. Introduction 206
II. Examining the Assumptions 207
III. Physical Properties of Cytoplasm (Measured) 215
IV. Concluding Remarks 231
References 232
Chapter 9. Intracellular Compartmentation of Organelles and Gradients of Low Molecular Weight Species 240
I. Introduction 240
II. Compartmentation of Mitochondria within Mammalian Cells 242
III. lntracellular Gradients of O2 245
IV. lntracellular Gradients of Metabolites and Substrates 252
V. Regional Compartmentation of Ions in Aqueous Cytoplasm in Mammalian Cells 260
VI. Concluding Remarks 265
References 266
Chapter 10. Macromolecular Compartmentation and Channeling 272
I. introduction 272
II. Enzyme Interactions 274
Ill. Metabolic Channeling 285
IV. Cross-Linking Processes 290
V. One Future Direction 292
References 293
Chapter 11. The State of Water in Biological Systems 298
I. Introduction 298
II. Osmotic Behavior of Polar Solutes–Introduction to the Osmotic Intercept 300
III. Mitochondria-The Experimental Model 302
IV. Osmotic Equilibria in Mitochondria 303
V. Nonelectrolyte Distributions in Mitochondria 307
VI. Solute Distribution as a Function of Matrix Volume 309
Vll. Discussion 313
Vlll. Concluding Remarks 317
References 318
Chapter 12. Mechanisms for Cytoplasmic Organization: An Overview 320
I. Introduction 320
II. Cytoplasm as a Biochemical Environment: Compartmentation Is a Fundamental Characteristic 321
III. Mechanisms, Models, and Dynamics for Establishing and Maintaining Cytoplasmic Organization 324
IV. Concluding Remarks 331
References 332
PART III: CYTOPLASM AND PHASE SEPARATION 336
Chapter 13. Can Cytoplasm Exist without Undergoing Phase Separation? 338
I. Introduction 338
II. Cytoplasm of the Lens of the Eye 339
Ill. Role of Bound Water 340
IV. Role of Insoluble Structures 342
V. Phase and Interface Volumes 342
VI. Experimental Approaches to Detecting Phases in Cytoplasm 343
VII. Conclusions 346
References 346
Chapter 14. Consequences of Phase Separation in Cytoplasm 348
I. Introduction: General Thesis 348
ll. Visualizing Phase Separation in Cytoplasm 349
III. Visualizing Biomaterials in Phase-Separated Cytoplasm 352
IV. Aspects of Cytoplasmic Organization 357
V. Concluding Remarks 358
References 360
Index 362

Partitioning and Concentrating Biomaterials in Aqueous Phase Systems


Göte Johansson; Harry Walter    Department of Biochemistry, University of Lund, S-22100, Lund, Sweden
Aqueous Phase Systems, Washington D.C. 20008

Abstract


Aqueous phase separation is a general phenomenon which occurs when structurally distinct water-soluble macromolecules are dissolved, above certain concentrations, in water. The number of aqueous phases obtained depends on the number of such distinct macromolecular species used. Aqueous two-phase systems, primarily those containing poly(ethylene glycol) and dextran, have been widely used for the separation of biomaterials (macromolecules, membranes, organelles, cells) by partitioning. The polymer and salt compositions and concentrations chosen greatly affect the physical properties of the phases. These, in turn, interact with the physical properties of biomaterials included in the phases and affect their partitioning. Specific extractions of biomaterials can be effected by including affinity ligands in the systems. The phase systems can also be used to obtain information on the surface properties of materials partitioned in them; to study interactions between biomaterials; and to concentrate such materials.

KEY WORDS

Affinity partitioning

Aqueous phase systems

Cells

Concentration of biomaterials

Membranes

Nucleic acids

Partitioning

Proteins

Purification

Separation

I Introduction


A Immiscible Phases


Aqueous phase separation generally occurs when structurally distinct water-soluble macromolecules are dissolved, above certain concentrations, in water. First described by Beijerinck about one hundred years ago (1896), two-polymer aqueous-aqueous two-phase systems were applied by Albertsson, starting in the 1950s, to partitioning biomaterials (Albertsson, 1986; Walter et al., 1985; Walter and Johansson, 1994; Zaslavsky, 1995). Thus, differential partitioning of components of a mixture between or among immiscible liquid phases, one of the classical separatory methods, became available for the separation and fractionation of labile biomaterials: macromolecules, membranes, organelles, and even cells.

B Partitioning between Liquid Phases and Its Use in the Separation of Mixtures


The separation of components of a mixture can be effected when they have different solubilities in the top and bottom phases of an immiscible phase system to which the mixture is added. The separation of two soluble components, for example, can be induced by mixing the phases, letting the phases settle and then physically separating them. Each phase, top or bottom, will be enriched with respect to the component which has a greater solubility in it. When the solubility of each component differs greatly in the two phases (i.e., one component is essentially soluble only in one phase and the other component only in the other) a virtually complete separation is obtained in a single, or bulk, extraction step. Smaller differences in the solubility of components in the two phases still permit their separation but require that multiple extraction steps be carried out [as, for example, in countercurrent distribution (CCD) (Åkerlund and Albertsson, 1994)]. In this procedure each of the phases, top and bottom, is reextracted, respectively, with bottom and top phases. The number of sequential extraction steps required to effect a separation is determined by the relative solubilities of the components in the two phases. The distribution of each material between the phases is quantitatively described by a partition coefficient, K, which is defined as the concentration of the material in the top phase/ concentration of material in the bottom phase.

C Aqueous Two-Phase and Multiphase Systems


Aqueous two-phase systems are formed, as indicated above, when two structurally distinct polymers are dissolved in water above certain concentrations. Immiscible aqueous multiphase systems can be obtained by increasing the number of different polymers used.

1 Partitioning of Biomaterials

The most widely used and studied aqueous two-phase systems contain dextran and poly(ethylene glycol) (PEG). These have been found to be mild and nondeleterious to biological materials and often even exhibit protective effects on materials partitioned in them. They have very low interfacial tensions; moderately low viscosities; densities close to that of water; and can be buffered and rendered isotonic, if necessary (Albertsson, 1986; Walter et al., 1985; Walter and Johansson, 1994).

Both soluble and particulate materials can be partitioned in these systems. While soluble materials partition according to their relative solubilities in the top and bottom phases, the partitioning of particulates depends on their relative affinity for the bulk phases and the interface (for discussion, see Walter et al., 1992). The partitioning of macromolecules and small particulates (e.g., viruses) is influenced by both surface properties and surface area. The partitioning of particulates with surface areas larger than about 0.2 μm2 appears to depend predominantly on surface properties (Walter et al., 1990). While soluble materials and small particulates partition between the bulk phases, particulates tend to partition, with increasing size, among the two bulk phases and the interface and, finally, between one bulk phase and the interface.

The partitioning of larger particulates is time-dependent and is thus measured at the shortest time after mixing deemed adequate for virtually complete phase settling. The time required for phase separation depends, among other things, on phase composition (e.g., polymers and salt used and their concentrations), on the volume ratio (top to bottom phase), and on the presence of the particulates themselves. The partitioning is usually described as the quantity of particulate in a bulk phase as a percentage of total particulate added, P.

The physical properties of the phases can be manipulated (as described below) so as to involve non-charge related, charge-associated, or biospecific groups as determinants of the partitioning behavior of the added biomaterial.

2 Concentration by Partitioning between Phases

Any material which, due to a change in the properties of the system, changes its partitioning from being distributed in both phases to being primarily in one phase (by altering partitioning conditions) will cause it to be concentrated. Concentration also results when a partitioning material is forced from a larger into a smaller phase. If the volume ratio is extreme and the collecting phase is small, concentration of several hundredfold can be obtained.

II Aqueous Phase Systems


The separation of a solvent such as water into two liquid phases by addition of two soluble polymers is a very general phenomenon. The polymers must however, distinctively differ in their chemical structure. The concentrations of polymers necessary decrease with increasing molecular weights. In the dextran-PEG systems, the concentration of water is normally 92–98% in the top phase and 80–90% in the bottom phase. With some polymer pairs, two-phase systems with up to 98% water in each phase have been obtained (Albertsson, 1986; Tjerneld and Johansson, 1990).

A Macromolecular Compositions and Aqueous Phase Separation


The formation of two phases in water has been observed for a great number of polymer pairs (Tjerneld and Johansson, 1990). Two synthetic polymers like PEG and polyvinylalcohol (PVA), which both consist of linear molecules, generate two phases at relatively high concentrations. The most used systems have been composed of one synthetic polymer, typically PEG, and one polysaccharide, e.g., dextran. The popularity of these systems is mainly due to phase formation at moderate concentration of polymers and the relatively rapid settling of the phases. Several systems based on two polysaccharides are known. Dextran and modified dextran, e.g., hydroxypropyl dextran, benzoyl dextran, or valeryl dextran, phase separate. Also the same derivative of dextran, e.g., benzoyl dextran, but with differing degrees of substitution may, when mixed, yield phase separation (Lu et al., 1994).

Proteins are known to form liquid-liquid two-phase systems (at certain concentrations) with a number of polymers. Synthetic polymers which have been used for protein precipitation, e.g., PEG, PVA, and poly(vinylpyrrolidone) (PVP), generate, at moderate concentrations, liquid systems with many proteins and protein mixtures (Johansson, 1996). Polysaccharides may also form two-phase systems with proteins (see chapter by Tolstoguzov, this volume). Certain proteins give rise to protein–protein aqueous two- phase systems (see chapter by Tolstoguzov, this volume) while others form aqueous two-phase systems composed of a protein-rich and a protein-poorphase (see chapter by Clark and Clark, this volume).

A third polymer added to a two-phase system will give rise to a third phase if the concentrations of polymers are high enough. When a third polymer is introduced at low concentration into a PEG-dextran solution that is sufficiently dilute to form a single phase, it may cause the phases to separate. At low concentration, the third polymer will distribute between the two...

Erscheint lt. Verlag 21.10.1999
Mitarbeit Herausgeber (Serie): Kwang W. Jeon
Sprache englisch
Themenwelt Medizin / Pharmazie Studium 1. Studienabschnitt (Vorklinik)
Naturwissenschaften Biologie Genetik / Molekularbiologie
Naturwissenschaften Biologie Zellbiologie
Technik
ISBN-10 0-08-085731-0 / 0080857310
ISBN-13 978-0-08-085731-2 / 9780080857312
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