How can biochemical reactions within cells differ from those in test tubes?

Minton, Allen P.

doi:10.1242/jcs.03063

Cited by 378 publications

(252 citation statements)

References 74 publications

(69 reference statements)

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“…4,5 However, multiple considerations led us to be cautious in pushing the interpretation of the in vivo data: First, our protocol was designed to err on the side of retaining viability of the cells exposed to urea by restricting the time of incubation as much as possible. Second, we recognized that a great number of urea-dependent phenomena could be taking place in the cells (stress responses, denaturation of other proteins, chaperone binding, etc.).…”

Section: Review Of Our In Vivo Folding and Aggregation Studiesmentioning

confidence: 99%

“…Factors that must be considered include interactions with other components in vivo (including chaperones) and macromolecular crowding, although the latter is predicted to accelerate the folding kinetics and not influence the unfolding kinetics. 4,5 These predictions were based, however, on neutral or repulsive interactions between the folding polypeptide and the crowding species. The presence of attractive interactions, as might be expected for chaperones, could lead to exactly the opposite effects.…”

Section: In Vitro Versus In Vivo Protein Stabilitymentioning

confidence: 99%

“…We have developed a fluorescence approach using From the Test Tube to the Cell: Exploring the Folding and Aggregation of a b-Clam Protein conformational dynamics and energetics of folding polypeptides, favoring compact states. 4,5 Moreover, proteins emerge vectorially from the ribosome with a rate comparable with the rates observed for fundamental steps in protein folding in vitro; the rate of translation in bacteria is *10-50 amino acids per second and in eukaryotes, 4-5 amino acids per second. Thus, the N-terminal regions of a growing polypeptide in vivo will explore conformational space before the C-terminal regions have emerged from the ribosome.…”

Section: Introductionmentioning

confidence: 95%

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From the test tube to the cell: Exploring the folding and aggregation of a β‐clam protein

Ignatova¹,

Krishnan²,

Bombardier³

et al. 2007

Biopolymers

106

126

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A crucial challenge in present biomedical research is the elucidation of how fundamental processes like protein folding and aggregation occur in the complex environment of the cell. Many new physico‐chemical factors like crowding and confinement must be considered, and immense technical hurdles must be overcome in order to explore these processes in vivo. Understanding protein misfolding and aggregation diseases and developing therapeutic strategies to these diseases demand that we gain mechanistic insight into behaviors and misbehaviors of proteins as they fold in vivo. We have developed a fluorescence approach using FlAsH labeling to study the thermodynamics of folding of a model β‐rich protein, cellular retinoic acid binding protein (CRABP) in Escherichia coli cells. The labeling approach has also enabled us to follow aggregation of a modified version of CRABP and chimeras between CRABP and huntingtin exon 1 with its glutamine repeat tract. In this article, we review our recent results using FlAsH labeling to study in‐vivo folding and present new observations that hint at fundamental differences between the thermodynamics and kinetics of protein folding in vivo and in vitro. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 88: 157–163, 2007. This article was originally published online as an accepted preprint. The ‘Published Online’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Section: Review Of Our In Vivo Folding and Aggregation Studiesmentioning

confidence: 99%

Section: In Vitro Versus In Vivo Protein Stabilitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 95%

See 1 more Smart Citation

From the test tube to the cell: Exploring the folding and aggregation of a β‐clam protein

Ignatova¹,

Krishnan²,

Bombardier³

et al. 2007

Biopolymers

106

126

View full text Add to dashboard Cite

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“…15 Beside changes of the dynamic behavior, a crowded environment can also change the rate of the association and adsorption of macromolecules. 31 It should be pointed out that, recently, it was proven that the slowing down of motion in living cells had previously been overestimated. 16 Theoretical treatment of the motion of objects in a crowded environment also results in a subdiffusive behavior.…”

Section: Introductionmentioning

confidence: 99%

Simulation of diffusion in a crowded environment

Polanowski

Sikorski

2014

Soft Matter

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We performed extensive and systematic simulation studies of two-dimensional fluid motion in a complex crowded environment. In contrast to other studies we focused on cooperative phenomena that occurred if the motion of particles takes place in a dense crowded system, which can be considered as a crude model of a cellular membrane. Our main goal was to answer the following question: how do the fluid molecules move in an environment with a complex structure, taking into account the fact that motions of fluid molecules are highly correlated. The dynamic lattice liquid (DLL) model, which can work at the highest fluid density, was employed. Within the frame of the DLL model we considered cooperative motion of fluid particles in an environment that contained static obstacles. The dynamic properties of the system as a function of the concentration of obstacles were studied. The subdiffusive motion of particles was found in the crowded system. The influence of hydrodynamics on the motion was investigated via analysis of the displacement in closed cooperative loops. The simulation and the analysis emphasize the influence of the movement correlation between moving particles and obstacles.

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“…The strong impact of environments on biomolecules already made some researchers wonder how relevant the learning from conformational studies of proteins in test tubes is to what the molecules do in natural settings. 1 Unlike a dilute solution, some intracellular compartments have macromolecules reaching 500 g/L in concentration. The conformation of proteins and other macromolecules sometimes differs greatly in these crowded environments from those in dilute, homogeneous solution.…”

Section: Introductionmentioning

confidence: 99%

Environmental Effects Dominate the Folding of Oligocholates in Solution, Surfactant Micelles, and Lipid Membranes

Cho

Zhao

2010

J. Am. Chem. Soc.

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Oligocholate foldamers with different numbers and locations of guanidinium−carboxylate salt bridges were synthesized. The salt bridges were introduced by incorporating arginine and glutamic acid residues into the foldamer sequence. The conformations of these foldamers were studied by fluorescence spectroscopy in homogeneous solution, anionic and nonionic micelles, and lipid bilayers. Environmental effects instead of inherent foldability were found to dominate the folding. As different noncovalent forces become involved in the conformations of the molecules, the best folder in one environment could turn into the worst in another. Preferential solvation was the main driving force for the folding of oligocholates in solution. The molecules behaved very differently in micelles and lipid bilayers, with the most critical factors controlling the folding−unfolding equilibrium being the solvation of ionic groups and the abilities of the surfactants/lipids to compete for the salt bridge. Because of their ability to fold into helices with a nonpolar exterior and a polar interior, the oligocholates could transport large hydrophilic molecules such as carboxyfluorescein across lipid bilayers. Both the conformational properties of the oligocholates and their binding with the guest were important to the transport efficiency. Abstract:Oligocholate foldamers with different numbers and locations of guanidinium-carboxylate salt bridges were synthesized. The salt bridges were introduced by incorporating arginine and glutamic acid residues into the foldamer sequence. The conformations of these foldamers were studied by fluorescence spectroscopy in homogeneous solution, anionic and nonionic micelles, and lipid bilayers. Environmental effects instead of inherent foldability were found to dominate the folding. As different noncovalent forces become involved in the conformations of the molecules, the best folder in one environment could turn into the worst in another. Preferential solvation was the main driving force for the folding of oligocholates in solution. The molecules behaved very differently in micelles and lipid bilayers, with the most critical factors controlling the folding-unfolding equilibrium being the solvation of ionic groups and the abilities of the surfactants/lipids to compete for the salt bridge. Because of their ability to fold into helices with a nonpolar exterior and a polar interior, the oligocholates could transport large hydrophilic molecules such as carboxyfluorescein across lipid bilayers. Both the conformational properties of the oligocholates and their binding with the guest were important to the transport efficiency.

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How can biochemical reactions within cells differ from those in test tubes?

Cited by 378 publications

References 74 publications

From the test tube to the cell: Exploring the folding and aggregation of a β‐clam protein

From the test tube to the cell: Exploring the folding and aggregation of a β‐clam protein

Simulation of diffusion in a crowded environment

Environmental Effects Dominate the Folding of Oligocholates in Solution, Surfactant Micelles, and Lipid Membranes

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