Enhancement of self-association of human spectrin by polyethylene glycol

Molecular crowding and RNA synergize to promote phase separation, microtubule interaction, and seeding of Tau condensates

Biomolecular condensation of the neuronal microtubule-associated protein Tau (MAPT) can be induced by coacervation with polyanions like RNA, or by molecular crowding. Tau condensates have been linked to both functional microtubule binding and pathological aggregation in neurodegenerative diseases. We find that molecular crowding and coacervation with RNA, two conditions likely coexisting in the cytosol, synergize to enable Tau condensation at physiological buffer conditions and to produce condensates with a strong affinity to charged surfaces. During condensate-mediated microtubule polymerization, their synergy enhances bundling and spatial arrangement of microtubules. We further show that different Tau condensates efficiently induce pathological Tau aggregates in cells, including accumulations at the nuclear envelope that correlate with nucleocytoplasmic transport deficits. Fluorescent lifetime imaging reveals different molecular packing densities of Tau in cellular accumulations and a condensate-like density for nuclear-envelope Tau. These findings suggest that a complex interplay between interaction partners, post-translational modifications, and molecular crowding regulates the formation and function of Tau condensates. Conditions leading to prolonged existence of Tau condensates may induce the formation of seeding-competent Tau and lead to distinct cellular Tau accumulations.

Molecular crowding and RNA catalysis

RNA enzymes or ribozymes catalyze some of the most important reactions in biology and are thought to have played a central role in the origin and evolution of life on earth. Catalytic function in RNA has evolved in crowded cellular environments that are different from dilute solutions in which most in vitro assays are performed. The presence of molecules such as amino acids, polypeptides, alcohols, and sugars in the cell introduces forces that modify the kinetics and thermodynamics of ribozyme-catalyzed reactions. Synthetic molecules are routinely used in in vitro studies to better approximate the properties of biomolecules under in vivo conditions. This review discusses the various forces that operate within simulated crowded solutions in the context of RNA structure, folding, and catalysis. It also explores ideas about how crowding could have been beneficial to the evolution of functional RNAs and the development of primitive cellular systems in a prebiotic milieu.

The effects of osmolytes and crowding on the pressure-induced dissociation and inactivation of dimeric LADH

Compatible osmolytes are able to efficiently modulate the oligomeric state, stability and activity of enzymes at high pressures.

Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications

Biomimetic microenvironments are key components to successful cell culture and tissue engineering in vitro. One of the most accurate biomimetic microenvironments is that made by the cells themselves. Cell-made microenvironments are most similar to the in vivo state as they are cell-specific and produced by the actual cells which reside in that specific microenvironment. However, cell-made microenvironments have been challenging to re-create in vitro due to the lack of extracellular matrix composition, volume and complexity which are required. By applying macromolecular crowding to current cell culture protocols, cell-made microenvironments, or cell-derived matrices, can be generated at significant rates in vitro. In this review, we will examine the causes and effects of macromolecular crowding and how it has been applied in several in vitro systems including tissue engineering.

Crowding effects on protein association: effect of interactions between crowding agents

The cell cytoplasm is a dense environment where the presence of inert cosolutes can significantly alter the rates of protein folding and protein association reactions. Most theoretical studies focus on hard sphere crowding agents and quantify the effect of excluded volume on reaction rates. In this work the effect of interactions between the crowding agents on the thermodynamics of protein association is studied using computer simulation. Three cases are considered, where the crowding agents are (i) hard spheres, (ii) hard spheres with additional attractive or repulsive interactions, and (iii) chains of hard spheres. Reactants and products of the protein association are modeled as hard spheres. Although crowding effects are sensitive to the shape of the reaction product, in most cases the excess free energy difference between the product and reactants (nonideality factor) is insensitive to the interactions between crowding agents, due to a cancellation of effects. The simulations therefore suggest that the hard sphere model of crowding agents has a surprisingly large regime of validity and should be sufficient for a qualitative understanding of the thermodynamics of crowding effects when the interactions of associating proteins with crowding agents other than excluded volume interactions are not significant.

The effect of the presence of globular proteins and elongated polymers on enzyme activity

We have studied the effect of a crowded (macromolecular) solution on reaction rates of the decarboxylating enzymes urease, pyruvate decarboxylase and glutamate decarboxylase. A variety of crowding agents were used including haemoglobin, lysozyme, various dextrans and polyethylene glycol. Enzyme reaction rates of all three enzymes show two different types of effect that separate the globular proteins from the polysaccharides/polymers. Increasing concentration of globular proteins caused a dramatic rise in enzyme activity up to 30% crowding concentration then the activity decreased, whereas the polymers caused a concentration dependent decrease in activity. The viscosities of the globular proteins were low compared to the polymers. The increased activity with proteins may be due to the decreased amount of free water, which leads to higher effective concentration of substrates, or to an increased oligomeric state by self-association. The lower activities of all enzymes with all agents at high concentrations may be explained by a decrease in rates of diffusion. An increase in protein crowding (decrease in cell water content) may contribute to pathological conditions including cataract and Alzheimer's disease.

Effects of inert volume-excluding macromolecules on protein fiber formation. II. Kinetic models for nucleated fiber growth

A sequential model for nucleated protein fiber formation is proposed that is similar in broad outline to models proposed previously (Thermodynamics of the Polymerization of Protein, Academic Press, New York, (1975); Biophys. J. 50 (1986) 583) but generalized to allow for thermodynamic nonideality resulting from a high degree of volume occupancy by inert macromolecular cosolutes (macromolecular crowding). The effect of volume occupancy on the rate of fiber formation is studied in the transition-state rate-limited regime through systematic variation of rate-limiting step (prenuclear oligomer formation, nucleus formation or fiber growth), shape of prenuclear oligomer, size of nucleus, extent of reversibility, nature of inert cosolute (hard globular particle or random coil polymer) and size of inert cosolute relative to that of fiber-forming protein. It is found that crowding can accelerate the rate of fiber formation by as much as several orders of magnitude. The extent of acceleration for a given degree of volume occupancy depends upon several factors, the most conspicuous of which is the stoichiometry of the nucleus. In contrast, the rate of redistribution of fiber length, which occurs on a much slower time scale than polymer formation, is found to be insensitive to the extent of crowding.

Noise-reduction through interaction in gene expression and biochemical reaction processes

We demonstrate that interaction in gene expression and biochemical reaction processes has a significant influence on reducing fluctuations. Especially, we have found that the interaction between synthesized proteins and background molecules can reduce the fluctuation level in gene expression, which is a counter example to the intuition that background factors disturb information processing in genetic networks by increasing the noise level. This fact also indicates that the macromolecular crowding observed in actual cells can contribute to reduce the noise level. In addition, the noise-reduction phenomenon is not limited to the interaction between the proteins and background molecules, but can be applied to other reactions such as a dimerization process and the coupling of reactions with large fluctuations by intrinsic noise. Finally, on the basis of these results, we propose a new and plausible method for reducing the fluctuations generated in synthesized genetic networks, and also discuss the applicability of this method to the stabilization of system dynamics by using a toggle switch model.

3D domain swapping: as domains continue to swap

Three-dimensional (3D) domain swapping creates a bond between two or more protein molecules as they exchange their identical domains. Since the term '3D domain swapping' was first used to describe the dimeric structure of diphtheria toxin, the database of domain-swapped proteins has greatly expanded. Analyses of the now about 40 structurally characterized cases of domain-swapped proteins reveal that most swapped domains are at either the N or C terminus and that the swapped domains are diverse in their primary and secondary structures. In addition to tabulating domain-swapped proteins, we describe in detail several examples of 3D domain swapping which show the swapping of more than one domain in a protein, the structural evidence for 3D domain swapping in amyloid proteins, and the flexibility of hinge loops. We also discuss the physiological relevance of 3D domain swapping and a possible mechanism for 3D domain swapping. The present state of knowledge leads us to suggest that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus. As domains continue to swap, this review attempts not only a summary of the known domain-swapped proteins, but also a framework for understanding future findings of 3D domain swapping.

Structures of the two 3D domain-swapped RNase A trimers

When concentrated in mildly acidic solutions, bovine pancreatic ribonuclease (RNase A) forms long-lived oligomers including two types of dimer, two types of trimer, and higher oligomers. In previous crystallographic work, we found that the major dimeric component forms by a swapping of the C-terminal beta-strands between the monomers, and that the minor dimeric component forms by swapping the N-terminal alpha-helices of the monomers. On the basis of these structures, we proposed that a linear RNase A trimer can form from a central molecule that simultaneously swaps its N-terminal helix with a second RNase A molecule and its C-terminal strand with a third molecule. Studies by dissociation are consistent with this model for the major trimeric component: the major trimer dissociates into both the major and the minor dimers, as well as monomers. In contrast, the minor trimer component dissociates into the monomer and the major dimer. This suggests that the minor trimer is cyclic, formed from three monomers that swap their C-terminal beta-strands into identical molecules. These conclusions are supported by cross-linking of lysyl residues, showing that the major trimer swaps its N-terminal helix, and the minor trimer does not. We verified by X-ray crystallography the proposed cyclic structure for the minor trimer, with swapping of the C-terminal beta-strands. This study thus expands the variety of domain-swapped oligomers by revealing the first example of a protein that can form both a linear and a cyclic domain-swapped oligomer. These structures permit interpretation of the enzymatic activities of the RNase A oligomers on double-stranded RNA.

Macromolecular crowding and its role as intracellular signalling of cell volume regulation

Macromolecular crowding has been proposed as a mechanism by means of which a cell can sense relatively small changes in volume or, more accurately, the concentration of intracellular solutes. According to the macromolecular theory, the kinetics and equilibria of enzymes can be greatly influenced by small changes in the concentration of ambient, inert macromolecules. A 10% change in the concentration of intracellular proteins can lead to changes of up to a factor of ten in the thermodynamic activity of putative molecular regulatory species, and consequently, the extent to which such regulator(s) may bind to and activate membrane-associated ion transporters. The aim of this review is to examine the concept of macromolecular crowding and how it profoundly affects macromolecular association in an intact cell with particular emphasis on its implication as a sensor and a mechanism through which cell volume is regulated.

Implications of macromolecular crowding for protein assembly

Recent studies have led to increased appreciation of the influence of excluded volume in solutions of high total macromolecular content ('macromolecular crowding') upon the various classes of reaction that lead to the assembly of proteins and protein complexes. In general, crowding is expected to stabilize native protein structure relative to less compact non-native structures and to favor the formation of functional complexes of native proteins. Under certain pathological conditions, 'overcrowding' may enhance the formation of nonfunctional aggregates of non-native protein (e.g. amyloid and inclusion bodies).

Influence of excluded volume upon macromolecular structure and associations in 'crowded' media

Results of experimental studies published since the last major review of excluded volume effects in biopolymer solutions in 1993 add to our appreciation of the scope and magnitude of such effects. Recent theoretical studies have improved incrementally our ability to understand and model excluded volume effects in simple model systems.