Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

Elcock, Adrian H.

doi:10.1016/j.sbi.2010.01.008

Cited by 268 publications

(236 citation statements)

References 87 publications

(112 reference statements)

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“…The role of such "chemical interactions" is a subject of debate also for proteins and PEG (13,26). Notably, the approach presented here (Eq.…”

Section: Significancementioning

confidence: 99%

“…The question of how the conformational distributions of IDPs respond to crowded environments is of particular current interest because IDPs have a vital role in cellular compartments and regions with very high local concentrations of proteins and RNA, such as RNA granules and nuclear pore complexes (22)(23)(24)(25). However, a quantitative comprehension of how the concentrations and sizes of the molecular crowding agents (or "crowders") affect IDPs is currently incomplete (26), especially for polymeric crowders. Here we use single-molecule spectroscopy to investigate the influence of crowding on the conformational distributions of IDPs, as a step toward a quantitative framework of how the polydisperse cellular environment affects these highly flexible molecules.…”

mentioning

confidence: 99%

“…S1) is available from monomeric ethylene glycol to degrees of polymerization of almost 1,000 (SI Appendix, Table S1) at sufficient purity for single-molecule experiments up to physiologically realistic volume fractions of crowder of ∼40% (30). PEG is widely used for biomedical applications (31) and for mimicking inert crowding agents (13,26). Previous work has shown that the conformational properties of IDPs strongly depend on their amino acid sequence composition and charge patterning (8,11,27,28,(32)(33)(34).…”

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confidence: 99%

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Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Soranno

Koenig

Borgia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

233

307

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Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu. A surprisingly large number of eukaryotic proteins either contain substantial unstructured regions or are entirely unfolded under physiological conditions (1, 2). These "intrinsically disordered proteins" (IDPs) are involved in many crucial cellular processes, such as transcription, translation, and signal transduction; their functional and conformational properties are thus of great interest for a wide range of biological questions. Important advances in understanding the structures of IDPs have been made over the past decade, especially with spectroscopic techniques, e.g., NMR (3, 4), single-molecule fluorescence (5-7), and with atomistic and coarse-grained molecular simulations (8-10). In contrast with the stable folded structures we are familiar with from 50 y of structural biology, IDPs comprise highly heterogeneous and dynamic ensembles of conformations, which either lack stable tertiary structure altogether or fold only on binding their cellular targets (4). Important components of the cellular environment that affect IDPs include not only specific cellular ligands, but also pH and the concentration of salts (11,12). An additional contribution that has been difficult to investigate experimentally comes from the large number of different solutes present in a cell that do not interact with an IDP specifically, but result in an environment that is densely filled with macromolecules and metabolites (12)(13)(14). Given their lack of persistent structure, the conformations of IDPs are expected to be particularly sensitive to the effects of such molecular crowding. Indeed, first experiments indicate that some IDPs gain structure upon crowding (15), whereas others do not (16-18), but may change their dimensions (19)(20)(21). The question of how the conformational distributions of IDPs respond to crowded environments is of particular current interest because IDPs have a vital role in cellular compartments and regions with very high local concentrations of proteins and RNA, such as RNA granules and nuclear pore complexes (22)(23)(24)(25). Howeve...

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“…The role of such "chemical interactions" is a subject of debate also for proteins and PEG (13,26). Notably, the approach presented here (Eq.…”

Section: Significancementioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Soranno

Koenig

Borgia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

233

307

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“…The resulting fit parameters will have a sound physical basis and can therefore provide information on unknown microscopic interactions. However, such an approach is still ambiguous, as pointed out by Elcock (2010); for dextran, a commonly used crowding agent, three different spherical approximations have been used to fit the SPT equation in three different experiments (Batra et al 2009a, b).…”

Section: Computational Model Of Protein-protein Interactions In a Cromentioning

confidence: 99%

Protein–protein interactions in a crowded environment

2013

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Protein-protein interactions are important in many essential biological functions, such as transcription, translation, and signal transduction. Much progress has been made in understanding protein-protein association in dilute solution via experimentation and simulation. Cells, however, contain various macromolecules, such as DNA, RNA, proteins, among many others, and a myriad of non-specific interactions (usually weak) are present between these cellular constituents. In this review article, we describe the important developments in recent years that have furthered our understanding and even allowed prediction of the consequences of macromolecular crowding on protein-protein interactions. We outline the development of our crowding theory that can predict the change in binding free energy due to crowding quantitatively for both repulsive and attractive protein-crowder interactions. One of the most important findings from our recent work is that weak attractive interactions between crowders and proteins can actually destabilize protein complex formation as opposed to the commonly assumed stabilizing effect predicted based on traditional crowding theories that only account for the entropicexcluded volume effects. We also discuss the implications of macromolecular crowding on the population of encounter versus specific native complex.

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“…Further, a recent report suggests that PEG preferentially interacts with a particular quadruplex conformation and that excluded volume effects are negligible [31]. Although the presence of PEG in solution clearly influences the conformation and stability of a DNA quadruplex, referring to it as a crowding agent is not recommended [31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

The Human Telomere Sequence, (TTAGGG)4, in the Absence and Presence of Cosolutes: A Spectroscopic Investigation

Sharma

Sheardy

2014

Molecules

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Abstract:Historically, biophysical studies of nucleic acids have been carried out under near ideal conditions, i.e., low buffer concentration (e.g., 10 mM phosphate), pH 7, low ionic strength (e.g., 100 mM) and, for optical studies, low concentrations of DNA (e.g., 1 × 10 −6 M). Although valuable structural and thermodynamic data have come out of these studies, the conditions, for the most, part, are inadequate to simulate realistic cellular conditions. The increasing interest in studying biomolecules under more cellular-like conditions prompted us to investigate the effect of osmotic stress on the structural and thermodynamic properties of DNA oligomers containing the human telomere sequence (TTAGGG). Here, we report the characterization of (TTAGGG) 4 in potassium phosphate buffer with increasing percent PEG (polyethylene glycol) or acetonitrile. In general, the presence of these cosolutes induces a conformational change from a unimolecular hybrid structure to a multimolecular parallel stranded structure. Hence, the structural change is accompanied with a change in the molecularity of quadruplex formation.

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Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

Cited by 268 publications

References 87 publications

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Protein–protein interactions in a crowded environment

The Human Telomere Sequence, (TTAGGG)4, in the Absence and Presence of Cosolutes: A Spectroscopic Investigation

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