Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding

Minton, Allen P.

doi:10.1002/bip.22163

Cited by 119 publications

(148 citation statements)

References 23 publications

(25 reference statements)

Supporting

Mentioning

141

Contrasting

Order By: Relevance

“…The expectation was that crowding enhances stability by favoring the compact native state over the ensemble of denatured states. Increased attention to transient, nonspecific protein-protein interactions (12)(13)(14)(15) has led both experimentalists (16)(17)(18)(19) and theoreticians (20)(21)(22) to recognize the effects of chemical interactions between crowder and test protein when assessing the net effect of macromolecular crowding. These weak, nonspecific interactions can reinforce or oppose the effect of hard-core repulsions, resulting in increased or decreased stability depending on the chemical nature of the test protein and crowder (23)(24)(25)(26).…”

mentioning

confidence: 99%

Residue level quantification of protein stability in living cells

Monteith¹,

Pielak

2014

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

107

178

View full text Add to dashboard Cite

Significance Proteins function in a sea of macromolecules within cells, but are traditionally studied under ideal conditions in vitro . The more details we amass from experiments performed in cells, the closer we will get to understanding fundamental aspects of protein chemistry in the cellular environment. In addition to furthering our essential knowledge of biochemistry, advancements in the field of macromolecular crowding will drive efforts to stabilize protein-based therapeutics. Here, we show that protein stability can be measured at the residue level in living cells without adding destabilizing cosolutes or heat.

show abstract

mentioning

confidence: 99%

Residue level quantification of protein stability in living cells

Monteith¹,

Pielak

2014

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

107

178

View full text Add to dashboard Cite

show abstract

“…Recent experimental results indicate that the presence of weak, nonspecific attractive interactions in the heterogeneous cellular environment can modulate or even dominate the effects of hardcore repulsion that are at the basis of molecular crowding (46)(47)(48). The role of such "chemical interactions" is a subject of debate also for proteins and PEG (13,26).…”

Section: Significancementioning

confidence: 99%

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.

231

307

View full text Add to dashboard Cite

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...

show abstract

“…They concluded with remarks encouraging the incorporation of non-specific chemical interactions. Minton (2013) also mentions the effects of hard and soft interactions on protein stability in his review on crowding and protein-protein interactions.…”

Section: Soft Interactions and Excluded Volumementioning

confidence: 99%

Soft interactions and crowding

2013

View full text Add to dashboard Cite

The intracellular milieu is complex, heterogeneous and crowded-an environment vastly different from dilute solutions in which most biophysical studies are performed. The crowded cytoplasm excludes about a third of the volume available to macromolecules in dilute solution. This excluded volume is the sum of two parts: steric repulsions and chemical interactions, also called soft interactions. Until recently, most efforts to understand crowding have focused on steric repulsions. Here, we summarize the results and conclusions from recent studies on macromolecular crowding, emphasizing the contribution of soft interactions to the equilibrium thermodynamics of protein stability. Despite their non-specific and weak nature, the large number of soft interactions present under many crowded conditions can sometimes overcome the stabilizing steric, excluded volume effect.

show abstract

Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding

Cited by 119 publications

References 23 publications

Residue level quantification of protein stability in living cells

Residue level quantification of protein stability in living cells

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

Soft interactions and crowding

Contact Info

Product

Resources

About