Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding.

ABSTRACT: The effect of cellular crowding was examined from molecular dynamics simulations of chymotrypsin inhibitor 2 (CI2) in the presence of either lysozyme or bovine serum albumin (BSA) crowder molecules as a complement to recent experimental studies of the same systems (Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. J. Am. Chem. Soc.2011, 133, 7116). The simulations confirm a destabilization and significantly slowed diffusion of CI2 in the presence of lysozyme and indicate that this observation is a result of extensive, nonspecific protein-protein interactions between CI2 and lysozyme. CI2 interacts much less with BSA crowders corresponding to a weak effect of crowding. Energetic analysis suggests an overall favorable crowding free energy in the presence of lysozyme, while weaker interactions with BSA appear to be unfavorable.

SUBMITTER: Feig M

PROVIDER: S-EPMC3257409 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding.

Feig Michael M Sugita Yuji Y

The journal of physical chemistry. B 20111212 1

The effect of cellular crowding was examined from molecular dynamics simulations of chymotrypsin inhibitor 2 (CI2) in the presence of either lysozyme or bovine serum albumin (BSA) crowder molecules as a complement to recent experimental studies of the same systems (Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. J. Am. Chem. Soc.2011, 133, 7116). The simulations confirm a destabilization and significantly slowed diffusion of CI2 in the presence of lysozyme and indicate that this observation i ...[more]

PMID: 22117862

Similar Datasets

Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.

Project description:Living cells contain diverse biopolymers, creating a heterogeneous crowding environment, the impact of which on RNA folding is poorly understood. Here, we have used single-molecule fluorescence resonance energy transfer to monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene glycol and yeast cell extract as crowding agents. As expected, polyethylene glycol stabilizes the docked, catalytically active state of the ribozyme, in part through excluded volume effects; unexpectedly, we found evidence that it additionally displays soft, non-specific interactions with the ribozyme. Yeast extract has a profound effect on folding at protein concentrations 1000-fold lower than found intracellularly, suggesting the dominance of specific interactions over volume exclusion. Gel shift assays and affinity pull-down followed by mass spectrometry identified numerous non-canonical RNA-binding proteins that stabilize ribozyme folding; the apparent chaperoning activity of these ubiquitous proteins significantly compensates for the low-counterion environment of the cell.

| S-EPMC5805602 | biostudies-literature

Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders.

Project description:Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral:7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each.

| S-EPMC7175338 | biostudies-literature

Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions.

Project description:Dihydrofolate reductase (DHFR) reduces dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. Due to its role in one carbon metabolism, chromosomal DHFR is the target of the antibacterial drug, trimethoprim. Resistance to trimethoprim has resulted in a type II DHFR that is not structurally related to the chromosomal enzyme target. Because of its metabolic significance, understanding DHFR kinetics and ligand binding behavior in more cell-like conditions, where the total macromolecule concentration can be as great as 300 mg/mL, is important. The progress-curve kinetics and ligand binding properties of the drug target (chromosomal E. coli DHFR) and the drug resistant (R67 DHFR) enzymes were studied in the presence of macromolecular cosolutes. There were varied effects on NADPH oxidation and binding to the two DHFRs, with some cosolutes increasing affinity and others weakening binding. However, DHF binding and reduction in both DHFRs decreased in the presence of all cosolutes. The decreased binding of ligands is mostly attributed to weak associations with the macromolecules, as opposed to crowder effects on the DHFRs. Computer simulations found weak, transient interactions for both ligands with several proteins. The net charge of protein cosolutes correlated with effects on NADP+ binding, with near neutral and positively charged proteins having more detrimental effects on binding. For DHF binding, effects correlated more with the size of binding pockets on the protein crowders. These nonspecific interactions between DHFR ligands and proteins predict that the in vivo efficiency of DHFRs may be much lower than expected from their in vitro rates.

| S-EPMC6589827 | biostudies-literature

Interactions between the protein barnase and co-solutes studied by NMR.

Project description:Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.

| S-EPMC10902301 | biostudies-literature

Preferential interactions between small solutes and the protein backbone: a computational analysis.

Project description:To improve our understanding of the effects of small solutes on protein stability, we conducted atomistic simulations to quantitatively characterize the interactions between two broadly used small solutes, urea and glycine betaine (GB), and a triglycine peptide, which is a good model for a protein backbone. Multiple solute concentrations were analyzed, and each solute-peptide-water ternary system was studied with approximately 200-300 ns of molecular dynamics simulations with the CHARMM force field. The comparison between calculated preferential interaction coefficients (Gamma(23)) and experimentally measured values suggests that semiquantitative agreement with experiments can be obtained if care is exercised to balance interactions among the solute, protein, and water. On the other hand, qualitatively incorrect (i.e., wrong sign in Gamma(23)) results can be obtained if a solute model is constructed by directly taking parameters for chemically similar groups from an existing force field. Such sensitivity suggests that small solute thermodynamic data can be valuable in the development of accurate force field models of biomolecules. Further decomposition of Gamma(23) into group contributions leads to additional insights regarding the effects of small solutes on protein stability. For example, use of the CHARMM force field predicts that urea preferentially interacts with not only amide groups in the peptide backbone but also aliphatic groups, suggesting a role for these interactions in urea-induced protein denaturation; quantitatively, however, it is likely that the CHARMM force field overestimates the interaction between urea and aliphatic groups. The results with GB support a simple thermodynamic model that assumes additivity of preferential interaction between GB and various biomolecular surfaces.

| S-EPMC3639130 | biostudies-literature

Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them.

Project description:The origins of the hydrophobic effect are widely thought to lie in structural changes of the water molecules surrounding a nonpolar solute. The spatial distribution functions of the water molecules surrounding benzene and cyclohexane computed previously from molecular dynamics simulations show a high density first hydration shell surrounding both solutes. In addition, benzene showed a strong preference for hydrogen bonding with two water molecules, one to each face of the benzene ring. The position data alone, however, do not describe the majority of orientational changes in the water molecules in the first hydration shells surrounding these solutes. In this paper, we measure the changes in orientation of the water molecules with respect to the solute through spatial orientation functions as well as radial/angular distribution functions. These data show that the water molecules hydrogen bonded to benzene have a strong orientation preference, whereas those around cyclohexane show a weaker tendency. In addition, the water-water interactions within and between the first two hydration shells were measured as a function of distance and "best" hydrogen bonding angle. Water molecules within the first hydration shell have increased hydrogen bonding structure; water molecules interacting across shell 1 and shell 2 have reduced hydrogen bonding structure.

| S-EPMC1100774 | biostudies-literature

The interplay between chemo-phoretic interactions and crowding in active colloids.

Project description:Many motile microorganisms communicate with each other and their environments via chemical signaling which leads to long-range interactions mediated by self-generated chemical gradients. However, consequences of the interplay between crowding and chemotactic interactions on their collective behavior remain poorly understood. In this work, we use Brownian dynamics simulations to investigate the effect of packing fraction on the formation of non-equilibrium structures in a monolayer of diffusiophoretic self-propelled colloids as a model for chemically active particles. Focusing on the case when a chemical field induces attractive positional and repulsive orientational interactions, we explore dynamical steady-states of active colloids of varying packing fractions and degrees of motility. In addition to collapsed, active gas, and dynamical clustering steady-states reported earlier for low packing fractions, a new phase-separated state emerges. The phase separation results from a competition between long-range diffusiophoretic interactions and motility and is observed at moderate activities and a wide range of packing fractions. Our analysis suggests that the fraction of particles in the largest cluster is a suitable order parameter for capturing the transition from an active gas and dynamical clustering states to a phase-separated state.

| S-EPMC10053041 | biostudies-literature

Competitive interactions of ligands and macromolecular crowders with maltose binding protein.

Project description:Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concentrations of proteins, polysaccharides, and other macromolecules. The influence of macromolecular crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak association of maltose binding protein (MBP) with a polysaccharide crowder Ficoll, and that this association effectively competes with the binding of the natural ligand, maltose. Titration data over wide ranges of maltose and Ficoll concentrations fit well with a three-state competitive binding model. Broadening of MBP (1)H-(15)N TROSY spectra by the addition of Ficoll indicates weak protein-crowder association, and subsequent recovery of sharp NMR peaks upon addition of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.

| S-EPMC3790770 | biostudies-literature

Non-specific Interactions Between Macromolecular Solutes in Concentrated Solution: Physico-Chemical Manifestations and Biochemical Consequences.

Project description:A general thermodynamic formulation of the effect of hard and soft non-specific intermolecular interactions upon reaction equilibria is summarized. A highly simplified quantitative model for non-specific intermolecular interaction is introduced. This model is used to illustrate how the magnitudes of attractive and repulsive components of the overall intermolecular interaction, and the balance between them, influence the concentration-dependent properties of a highly concentrated solution of a single macromolecular solute. The properties calculated using the results of computer simulation and an approximate analytical model are found to agree qualitatively with the results of experimental measurements on protein solutions over a broad range of concentration.

| S-EPMC6424865 | biostudies-literature

Extended surfaces modulate hydrophobic interactions of neighboring solutes.

Project description:Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affects hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from subnanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects--the physics encoded in Lum-Chandler-Weeks theory [Lum K, Chandler D, Weeks JD (1999) J Phys Chem B 103:4570-4577]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.

| S-EPMC3203787 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data