Статті в журналах: "Proteins crowding"

1

Zhou, Huan-Xiang. "Crowding Effects of Membrane Proteins." Journal of Physical Chemistry B 113, no. 23 (June 11, 2009): 7995–8005. http://dx.doi.org/10.1021/jp8107446.

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2

Rhoades, Elizabeth. "Proteins: Disorder, Folding, and Crowding." Biophysical Journal 117, no. 1 (July 2019): 3–4. http://dx.doi.org/10.1016/j.bpj.2019.06.014.

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3

Snead, Wilton T., Carl C. Hayden, Avinash K. Gadok, Chi Zhao, Eileen M. Lafer, Padmini Rangamani, and Jeanne C. Stachowiak. "Membrane fission by protein crowding." Proceedings of the National Academy of Sciences 114, no. 16 (April 3, 2017): E3258—E3267. http://dx.doi.org/10.1073/pnas.1616199114.

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Membrane fission, which facilitates compartmentalization of biological processes into discrete, membrane-bound volumes, is essential for cellular life. Proteins with specific structural features including constricting rings, helical scaffolds, and hydrophobic membrane insertions are thought to be the primary drivers of fission. In contrast, here we report a mechanism of fission that is independent of protein structure—steric pressure among membrane-bound proteins. In particular, random collisions among crowded proteins generate substantial pressure, which if unbalanced on the opposite membrane surface can dramatically increase membrane curvature, leading to fission. Using the endocytic protein epsin1 N-terminal homology domain (ENTH), previously thought to drive fission by hydrophobic insertion, our results show that membrane coverage correlates equally with fission regardless of the hydrophobicity of insertions. Specifically, combining FRET-based measurements of membrane coverage with multiple, independent measurements of membrane vesiculation revealed that fission became spontaneous as steric pressure increased. Further, fission efficiency remained equally potent when helices were replaced by synthetic membrane-binding motifs. These data challenge the view that hydrophobic insertions drive membrane fission, suggesting instead that the role of insertions is to anchor proteins strongly to membrane surfaces, amplifying steric pressure. In line with these conclusions, even green fluorescent protein (GFP) was able to drive fission efficiently when bound to the membrane at high coverage. Our conclusions are further strengthened by the finding that intrinsically disordered proteins, which have large hydrodynamic radii yet lack a defined structure, drove fission with substantially greater potency than smaller, structured proteins.

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4

Zosel, Franziska, Andrea Soranno, Karin J. Buholzer, Daniel Nettels, and Benjamin Schuler. "Depletion interactions modulate the binding between disordered proteins in crowded environments." Proceedings of the National Academy of Sciences 117, no. 24 (June 2, 2020): 13480–89. http://dx.doi.org/10.1073/pnas.1921617117.

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Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of macromolecular crowding on the interactions of IDPs with their cellular targets. Here, we investigate the influence of crowding on the interaction between two IDPs that fold upon binding, with polyethylene glycol as a crowding agent. Single-molecule spectroscopy allows us to quantify the effects of crowding on a comprehensive set of observables simultaneously: the equilibrium stability of the complex, the association and dissociation kinetics, and the microviscosity, which governs translational diffusion. We show that a quantitative and coherent explanation of all observables is possible within the framework of depletion interactions if the polymeric nature of IDPs and crowders is incorporated based on recent theoretical developments. The resulting integrated framework can also rationalize important functional consequences, for example, that the interaction between the two IDPs is less enhanced by crowding than expected for folded proteins of the same size.

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5

Wei, Jiachen, and Fan Song. "Association equilibria for proteins interacted with crowders of short-range attraction in crowded environment." International Journal of Modern Physics B 31, no. 03 (January 23, 2017): 1750007. http://dx.doi.org/10.1142/s0217979217500072.

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Based on a very simple coarse-grained colloidal model, here we implement an effective hard-sphere theory and numerical simulation to capture the general features of the association equilibria for globular proteins in crowded environment. We measure the activity coefficient, i.e., the deviation from ideal behavior of protein solution, and the crowding factor, i.e., the contribution of crowders to the association equilibria, for proteins in macromolecular crowding. The results show that the association balance in macromolecular crowding depends sensitively on the magnitude of protein–crowder attraction and the relative size of reactant to crowding agent. Since our coarse-grained model is irrelevant to the microscopic details of the molecules, it can be applied to the control of the association equilibria of many globular proteins such as bovine serum albumin, crystallin and lysozyme.

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6

Horton, Margaret R., Felix Höfling, Joachim O. Rädler, and Thomas Franosch. "Development of anomalous diffusion among crowding proteins." Soft Matter 6, no. 12 (2010): 2648. http://dx.doi.org/10.1039/b924149c.

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7

Banks, Daniel S., and Cécile Fradin. "Anomalous Diffusion of Proteins Due to Molecular Crowding." Biophysical Journal 89, no. 5 (November 2005): 2960–71. http://dx.doi.org/10.1529/biophysj.104.051078.

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8

Makowski, Lee, Diane J. Rodi, Suneeta Mandava, David D. L. Minh, David B. Gore, and Robert F. Fischetti. "Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins." Journal of Molecular Biology 375, no. 2 (January 2008): 529–46. http://dx.doi.org/10.1016/j.jmb.2007.07.075.

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9

Candotti, Michela, and Modesto Orozco. "The Differential Response of Proteins to Macromolecular Crowding." PLOS Computational Biology 12, no. 7 (July 29, 2016): e1005040. http://dx.doi.org/10.1371/journal.pcbi.1005040.

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10

Perham, Michael, Loren Stagg, and Pernilla Wittung-Stafshede. "Macromolecular crowding increases structural content of folded proteins." FEBS Letters 581, no. 26 (October 1, 2007): 5065–69. http://dx.doi.org/10.1016/j.febslet.2007.09.049.

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11

Dias, Rita S. "Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model." Polymers 11, no. 7 (June 29, 2019): 1102. http://dx.doi.org/10.3390/polym11071102.

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Bacterial cells do not have a nuclear membrane that encompasses and isolates the genetic material. In addition, they do not possess histone proteins, which are responsible for the first levels of genome condensation in eukaryotes. Instead, there is a number of more or less specific nucleoid-associated proteins that induce DNA bridging, wrapping and bending. Many of these proteins self-assemble into oligomers. The crowded environment of cells is also believed to contribute to DNA condensation due to excluded volume effects. Ribosomes are protein-RNA complexes found in large concentrations in the cytosol of cells. They are overall negatively charged and some DNA-binding proteins have been reported to also bind to ribosomes. Here the effect of protein self-association on DNA condensation and stability of DNA-protein complexes is explored using Monte Carlo simulations and a simple coarse-grained model. The DNA-binding proteins are described as positively charged dimers with the same linear charge density as the DNA, described using a bead and spring model. The crowding molecules are simply described as hard-spheres with varying charge density. It was found that applying a weak attractive potential between protein dimers leads to their association in the vicinity of the DNA (but not in its absence), which greatly enhances the condensation of the model DNA. The presence of neutral crowding agents does not affect the DNA conformation in the presence or absence of protein dimers. For weakly self-associating proteins, the presence of negatively charged crowding particles induces the dissociation of the DNA-protein complex due to the partition of the proteins between the DNA and the crowders. Protein dimers with stronger association potentials, on the other hand, stabilize the nucleoid, even in the presence of highly charged crowders. The interactions between protein dimers and crowding agents are not completely prevented and a few crowding molecules typically bind to the nucleoid.

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12

Scott, Shane, Cynthia Shaheen, Brendon McGuinness, Kimberly Metera, Fedor Kouzine, David Levens, Craig J. Benham, and Sabrina Leslie. "Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules." Nucleic Acids Research 47, no. 12 (May 20, 2019): 6360–68. http://dx.doi.org/10.1093/nar/gkz408.

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Abstract DNA unwinding is an important cellular process involved in DNA replication, transcription and repair. In cells, molecular crowding caused by the presence of organelles, proteins, and other molecules affects numerous internal cellular structures. Here, we visualize plasmid DNA unwinding and binding dynamics to an oligonucleotide probe as functions of ionic strength, crowding agent concentration, and crowding agent species using single-molecule CLiC microscopy. We demonstrate increased probe–plasmid interaction over time with increasing concentration of 8 kDa polyethylene glycol (PEG), a crowding agent. We show decreased probe–plasmid interactions as ionic strength is increased without crowding. However, when crowding is introduced via 10% 8 kDa PEG, interactions between plasmids and oligos are enhanced. This is beyond what is expected for normal in vitro conditions, and may be a critically important, but as of yet unknown, factor in DNA’s proper biological function in vivo. Our results show that crowding has a strong effect on the initial concentration of unwound plasmids. In the dilute conditions used in these experiments, crowding does not impact probe–plasmid interactions once the site is unwound.

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13

Chebotareva, Natalia A., Svetlana G. Roman, Vera A. Borzova, Tatiana B. Eronina, Valeriya V. Mikhaylova, and Boris I. Kurganov. "Chaperone-Like Activity of HSPB5: The Effects of Quaternary Structure Dynamics and Crowding." International Journal of Molecular Sciences 21, no. 14 (July 13, 2020): 4940. http://dx.doi.org/10.3390/ijms21144940.

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Small heat-shock proteins (sHSPs) are ATP-independent molecular chaperones that interact with partially unfolded proteins, preventing their aberrant aggregation, thereby exhibiting a chaperone-like activity. Dynamics of the quaternary structure plays an important role in the chaperone-like activity of sHSPs. However, relationship between the dynamic structure of sHSPs and their chaperone-like activity remains insufficiently characterized. Many factors (temperature, ions, a target protein, crowding etc.) affect the structure and activity of sHSPs. The least studied is an effect of crowding on sHSPs activity. In this work the chaperone-like activity of HSPB5 was quantitatively characterized by dynamic light scattering using two test systems, namely test systems based on heat-induced aggregation of muscle glycogen phosphorylase b (Phb) at 48 °C and dithiothreitol-induced aggregation of α-lactalbumin at 37 °C. Analytical ultracentrifugation was used to control the oligomeric state of HSPB5 and target proteins. The possible anti-aggregation functioning of suboligomeric forms of HSPB5 is discussed. The effect of crowding on HSPB5 anti-aggregation activity was characterized using Phb as a target protein. The duration of the nucleation stage was shown to decrease with simultaneous increase in the relative rate of aggregation of Phb in the presence of HSPB5 under crowded conditions. Crowding may subtly modulate sHSPs activity.

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14

Borzova, Vera A., Svetlana G. Roman, Anastasiya V. Pivovarova, and Natalia A. Chebotareva. "Effects of Molecular Crowding and Betaine on HSPB5 Interactions, with Target Proteins Differing in the Quaternary Structure and Aggregation Mechanism." International Journal of Molecular Sciences 23, no. 23 (December 6, 2022): 15392. http://dx.doi.org/10.3390/ijms232315392.

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The aggregation of intracellular proteins may be enhanced under stress. The expression of heat-shock proteins (HSPs) and the accumulation of osmolytes are among the cellular protective mechanisms in these conditions. In addition, one should remember that the cell environment is highly crowded. The antiaggregation activity of HSPB5 and the effect on it of either a crowding agent (polyethylene glycol (PEG)) or an osmolyte (betaine), or their mixture, were tested on the aggregation of two target proteins that differ in the order of aggregation with respect to the protein: thermal aggregation of glutamate dehydrogenase and DTT-induced aggregation of lysozyme. The kinetic analysis of the dynamic light-scattering data indicates that crowding can decrease the chaperone-like activity of HSPB5. Nonetheless, the analytical ultracentrifugation shows the protective effect of HSPB5, which retains protein aggregates in a soluble state. Overall, various additives may either improve or impair the antiaggregation activity of HSPB5 against different protein targets. The mixed crowding arising from the presence of PEG and 1 M betaine demonstrates an extraordinary effect on the oligomeric state of protein aggregates. The shift in the equilibrium of HSPB5 dynamic ensembles allows for the regulation of its antiaggregation activity. Crowding can modulate HSPB5 activity by affecting protein–protein interactions.

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15

Demosthene, Bryan, Myeongsang Lee, Ryan R. Marracino, James B. Heidings, and Ellen Hyeran Kang. "Molecular Basis for Actin Polymerization Kinetics Modulated by Solution Crowding." Biomolecules 13, no. 5 (May 2, 2023): 786. http://dx.doi.org/10.3390/biom13050786.

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Actin polymerization drives cell movement and provides cells with structural integrity. Intracellular environments contain high concentrations of solutes, including organic compounds, macromolecules, and proteins. Macromolecular crowding has been shown to affect actin filament stability and bulk polymerization kinetics. However, the molecular mechanisms behind how crowding influences individual actin filament assembly are not well understood. In this study, we investigated how crowding modulates filament assembly kinetics using total internal reflection fluorescence (TIRF) microscopy imaging and pyrene fluorescence assays. The elongation rates of individual actin filaments analyzed from TIRF imaging depended on the type of crowding agent (polyethylene glycol, bovine serum albumin, and sucrose) as well as their concentrations. Further, we utilized all-atom molecular dynamics (MD) simulations to evaluate the effects of crowding molecules on the diffusion of actin monomers during filament assembly. Taken together, our data suggest that solution crowding can regulate actin assembly kinetics at the molecular level.

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16

Kim, Youngchan, and Jeetain Mittal. "Crowding Induced Coil-Globule Transitions of Intrinsically Disordered Proteins." Biophysical Journal 112, no. 3 (February 2017): 511a. http://dx.doi.org/10.1016/j.bpj.2016.11.2764.

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17

Qu, Youxing, and D. W. Bolen. "Efficacy of macromolecular crowding in forcing proteins to fold." Biophysical Chemistry 101-102 (December 2002): 155–65. http://dx.doi.org/10.1016/s0301-4622(02)00148-5.

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18

Gorensek-Benitez, Annelise H., Bryan Kirk, and Jeffrey K. Myers. "Protein Fibrillation under Crowded Conditions." Biomolecules 12, no. 7 (July 6, 2022): 950. http://dx.doi.org/10.3390/biom12070950.

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Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.

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19

André, Alain A. M., and Evan Spruijt. "Liquid–Liquid Phase Separation in Crowded Environments." International Journal of Molecular Sciences 21, no. 16 (August 17, 2020): 5908. http://dx.doi.org/10.3390/ijms21165908.

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Biomolecular condensates play a key role in organizing cellular fluids such as the cytoplasm and nucleoplasm. Most of these non-membranous organelles show liquid-like properties both in cells and when studied in vitro through liquid–liquid phase separation (LLPS) of purified proteins. In general, LLPS of proteins is known to be sensitive to variations in pH, temperature and ionic strength, but the role of crowding remains underappreciated. Several decades of research have shown that macromolecular crowding can have profound effects on protein interactions, folding and aggregation, and it must, by extension, also impact LLPS. However, the precise role of crowding in LLPS is far from trivial, as most condensate components have a disordered nature and exhibit multiple weak attractive interactions. Here, we discuss which factors determine the scope of LLPS in crowded environments, and we review the evidence for the impact of macromolecular crowding on phase boundaries, partitioning behavior and condensate properties. Based on a comparison of both in vivo and in vitro LLPS studies, we propose that phase separation in cells does not solely rely on attractive interactions, but shows important similarities to segregative phase separation.

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20

Snead, Wilton T., Wade F. Zeno, Grace Kago, Ryan W. Perkins, J. Blair Richter, Chi Zhao, Eileen M. Lafer, and Jeanne C. Stachowiak. "BAR scaffolds drive membrane fission by crowding disordered domains." Journal of Cell Biology 218, no. 2 (November 30, 2018): 664–82. http://dx.doi.org/10.1083/jcb.201807119.

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Cellular membranes are continuously remodeled. The crescent-shaped bin-amphiphysin-rvs (BAR) domains remodel membranes in multiple cellular pathways. Based on studies of isolated BAR domains in vitro, the current paradigm is that BAR domain–containing proteins polymerize into cylindrical scaffolds that stabilize lipid tubules. But in nature, proteins that contain BAR domains often also contain large intrinsically disordered regions. Using in vitro and live cell assays, here we show that full-length BAR domain–containing proteins, rather than stabilizing membrane tubules, are instead surprisingly potent drivers of membrane fission. Specifically, when BAR scaffolds assemble at membrane surfaces, their bulky disordered domains become crowded, generating steric pressure that destabilizes lipid tubules. More broadly, we observe this behavior with BAR domains that have a range of curvatures. These data suggest that the ability to concentrate disordered domains is a key driver of membrane remodeling and fission by BAR domain–containing proteins.

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21

Al-Ayoubi, S. R., P. H. Schummel, M. Golub, J. Peters, and R. Winter. "Influence of cosolvents, self-crowding, temperature and pressure on the sub-nanosecond dynamics and folding stability of lysozyme." Physical Chemistry Chemical Physics 19, no. 22 (2017): 14230–37. http://dx.doi.org/10.1039/c7cp00705a.

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22

Ross, Murial L., Jeffrey Kunkel, Steven Long, and Prashanth Asuri. "Combined Effects of Confinement and Macromolecular Crowding on Protein Stability." International Journal of Molecular Sciences 21, no. 22 (November 12, 2020): 8516. http://dx.doi.org/10.3390/ijms21228516.

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Confinement and crowding have been shown to affect protein fates, including folding, functional stability, and their interactions with self and other proteins. Using both theoretical and experimental studies, researchers have established the independent effects of confinement or crowding, but only a few studies have explored their effects in combination; therefore, their combined impact on protein fates is still relatively unknown. Here, we investigated the combined effects of confinement and crowding on protein stability using the pores of agarose hydrogels as a confining agent and the biopolymer, dextran, as a crowding agent. The addition of dextran further stabilized the enzymes encapsulated in agarose; moreover, the observed increases in enhancements (due to the addition of dextran) exceeded the sum of the individual enhancements due to confinement and crowding. These results suggest that even though confinement and crowding may behave differently in how they influence protein fates, these conditions may be combined to provide synergistic benefits for protein stabilization. In summary, our study demonstrated the successful use of polymer-based platforms to advance our understanding of how in vivo like environments impact protein function and structure.

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23

Tokuriki, N., T. Yomo, Y. Katakura, K. Ogasawara, K. Yutani, and I. Urabe. "Crowding effect of proteins with random sequence in polyethylene glycol." Seibutsu Butsuri 40, supplement (2000): S172. http://dx.doi.org/10.2142/biophys.40.s172_2.

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24

Li, Chao, Xiangxiang Zhang, Mingdong Dong, and Xiaojun Han. "Progress on Crowding Effect in Cell-like Structures." Membranes 12, no. 6 (June 3, 2022): 593. http://dx.doi.org/10.3390/membranes12060593.

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Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.

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25

Mondal, Somnath, Ravula Thirupathi, and Hanudatta S. Atreya. "Carbon quantum dots as a macromolecular crowder." RSC Advances 5, no. 6 (2015): 4489–92. http://dx.doi.org/10.1039/c4ra14019b.

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26

TAKAGI, Fumiko, and Syoji TAKADA. "Structure formation of proteins and "Molecular crowding" : Molecular dynamics simulation." Seibutsu Butsuri 41, supplement (2001): S175. http://dx.doi.org/10.2142/biophys.41.s175_4.

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27

Wojciechowski, M., and Marek Cieplak. "Effects of confinement and crowding on folding of model proteins." Biosystems 94, no. 3 (December 2008): 248–52. http://dx.doi.org/10.1016/j.biosystems.2008.06.016.

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28

Sulmann, Stefan, Daniele Dell'Orco, Valerio Marino, Petra Behnen, and Karl-Wilhelm Koch. "Conformational Changes in Calcium-Sensor Proteins under Molecular Crowding Conditions." Chemistry - A European Journal 20, no. 22 (March 27, 2014): 6756–62. http://dx.doi.org/10.1002/chem.201402146.

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29

Dey, Pinki, and Arnab Bhattacherjee. "Disparity in anomalous diffusion of proteins searching for their target DNA sites in a crowded medium is controlled by the size, shape and mobility of macromolecular crowders." Soft Matter 15, no. 9 (2019): 1960–69. http://dx.doi.org/10.1039/c8sm01933a.

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30

BESSA RAMOS, ESIO, KATHELIJNE WINTRAECKEN, ANS GEERLING, and RENKO DE VRIES. "SYNERGY OF DNA-BENDING NUCLEOID PROTEINS AND MACROMOLECULAR CROWDING IN CONDENSING DNA." Biophysical Reviews and Letters 02, no. 03n04 (October 2007): 259–65. http://dx.doi.org/10.1142/s1793048007000556.

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Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell.

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31

Byun, Wan Gi, Jihye Lee, Seungtaek Kim, and Seung Bum Park. "Harnessing stress granule formation by small molecules to inhibit the cellular replication of SARS-CoV-2." Chemical Communications 57, no. 93 (2021): 12476–79. http://dx.doi.org/10.1039/d1cc05508a.

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Small-molecule enhancers of cellular stress granules were identified by observing molecular crowding of proteins and RNAs in a time-dependent manner. Hit molecules inhibited the replication of SARS-CoV-2 by inducing stress granule formation.

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32

Qin, Sanbo, and Huan-Xiang Zhou. "Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins." Journal of Physical Chemistry Letters 4, no. 20 (September 30, 2013): 3429–34. http://dx.doi.org/10.1021/jz401817x.

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33

Cino, Elio A., Mikko Karttunen, and Wing-Yiu Choy. "Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins." PLoS ONE 7, no. 11 (November 26, 2012): e49876. http://dx.doi.org/10.1371/journal.pone.0049876.

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34

Wei, Yuzhang, Isabel Mayoral-Delgado, Nicolas A. Stewart, and Marcus K. Dymond. "Macromolecular crowding and membrane binding proteins: The case of phospholipase A1." Chemistry and Physics of Lipids 218 (January 2019): 91–102. http://dx.doi.org/10.1016/j.chemphyslip.2018.12.006.

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35

Lemetti, Laura, Sami-Pekka Hirvonen, Dmitrii Fedorov, Piotr Batys, Maria Sammalkorpi, Heikki Tenhu, Markus B. Linder, and A. Sesilja Aranko. "Molecular crowding facilitates assembly of spidroin-like proteins through phase separation." European Polymer Journal 112 (March 2019): 539–46. http://dx.doi.org/10.1016/j.eurpolymj.2018.10.010.

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36

de Vries, Renko. "DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins." Biochimie 92, no. 12 (December 2010): 1715–21. http://dx.doi.org/10.1016/j.biochi.2010.06.024.

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37

Shahid, Sumra, Ikramul Hasan, Faizan Ahmad, Md Imtaiyaz Hassan, and Asimul Islam. "Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder." Biomolecules 9, no. 9 (September 12, 2019): 477. http://dx.doi.org/10.3390/biom9090477.

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There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.

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38

Gupta, Munishwar Nath, and Vladimir N. Uversky. "Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins." International Journal of Molecular Sciences 24, no. 3 (January 26, 2023): 2424. http://dx.doi.org/10.3390/ijms24032424.

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Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.

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39

Bokvist, Marcus, and Gerhard Gröbner. "Misfolding of Amyloidogenic Proteins at Membrane Surfaces: The Impact of Macromolecular Crowding." Journal of the American Chemical Society 129, no. 48 (December 2007): 14848–49. http://dx.doi.org/10.1021/ja076059o.

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40

Cheung, M. S., D. Klimov, and D. Thirumalai. "Molecular crowding enhances native state stability and refolding rates of globular proteins." Proceedings of the National Academy of Sciences 102, no. 13 (March 21, 2005): 4753–58. http://dx.doi.org/10.1073/pnas.0409630102.

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41

Houser, Justin R., David J. Busch, David R. Bell, Brian Li, Pengyu Ren, and Jeanne C. Stachowiak. "The impact of physiological crowding on the diffusivity of membrane bound proteins." Soft Matter 12, no. 7 (2016): 2127–34. http://dx.doi.org/10.1039/c5sm02572a.

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42

Roman, Marisa I., Guoliang Yang, and Frank Ferrone. "Non Linear Effects of Macromolecular Crowding on the Mechanical Unfolding of Proteins." Biophysical Journal 104, no. 2 (January 2013): 566a. http://dx.doi.org/10.1016/j.bpj.2012.11.3138.

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43

Krepel, Dana, and Yaakov Levy. "Intersegmental transfer of proteins between DNA regions in the presence of crowding." Physical Chemistry Chemical Physics 19, no. 45 (2017): 30562–69. http://dx.doi.org/10.1039/c7cp05251k.

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Intersegmental transfer that involves direct relocation of a DNA-binding protein from one nonspecific DNA site to another was previously shown to contribute to speeding up the identification of the DNA target site.

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44

Goldenberg, David P., and Brian Argyle. "Self Crowding of Globular Proteins Studied by Small-Angle X-Ray Scattering." Biophysical Journal 106, no. 4 (February 2014): 895–904. http://dx.doi.org/10.1016/j.bpj.2013.12.004.

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45

Kumar, Rajesh, Rajesh Kumar, Deepak Sharma, Mansi Garg, Vinay Kumar, and Mukesh Chand Agarwal. "Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1866, no. 11 (November 2018): 1102–14. http://dx.doi.org/10.1016/j.bbapap.2018.08.012.

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46

Garner, M. M., and M. B. Burg. "Macromolecular crowding and confinement in cells exposed to hypertonicity." American Journal of Physiology-Cell Physiology 266, no. 4 (April 1, 1994): C877—C892. http://dx.doi.org/10.1152/ajpcell.1994.266.4.c877.

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The nonideal properties of solutions containing high concentrations of macromolecules can result in enormous increases in the activity of the individual macromolecules. It has been proposed that molecular crowding and confinement occur in cells and are major determinants of the activity of the proteins and other intracellular macromolecules. This concept has important implications for cell volume regulation because, under crowded conditions, relatively small changes in concentration, consequent to alterations of water content, lead to large changes in macromolecular activity. This review considers several aspects of macromolecular crowding and confinement, including: 1) the physical chemical principles involved; 2) in vitro demonstrations of the effects; 3) relation to water activity; 4) estimates of the actual intracellular activity of water and macromolecules; 5) relation to osmotic regulation in various types of cells, including bacteria, red blood cells, and complex nucleated cells; and 6) the relation to inorganic ions and organic osmolytes in cells stressed by hypertonicity. We conclude that, while there is compelling evidence for important effects of molecular crowding in vitro and in red blood cells, the role of macromolecular crowding and confinement in osmotic regulation of more complex cells is an open question that deserves the extensive attention it is currently receiving.

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47

Yang, Yin, Shen-Na Chen, Feng Yang, Xia-Yan Li, Akiva Feintuch, Xun-Cheng Su, and Daniella Goldfarb. "In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy." Proceedings of the National Academy of Sciences 117, no. 34 (August 11, 2020): 20566–75. http://dx.doi.org/10.1073/pnas.2005779117.

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The complexity of the cellular medium can affect proteins’ properties, and, therefore, in-cell characterization of proteins is essential. We explored the stability and conformation of the first baculoviral IAP repeat (BIR) domain of X chromosome-linked inhibitor of apoptosis (XIAP), BIR1, as a model for a homodimer protein in human HeLa cells. We employed double electron–electron resonance (DEER) spectroscopy and labeling with redox stable and rigid Gd3+spin labels at three representative protein residues, C12 (flexible region), E22C, and N28C (part of helical residues 26 to 31) in the N-terminal region. In contrast to predictions by excluded-volume crowding theory, the dimer–monomer dissociation constantKDwas markedly higher in cells than in solution and dilute cell lysate. As expected, this increase was partially recapitulated under conditions of high salt concentrations, given that conserved salt bridges at the dimer interface are critically required for association. Unexpectedly, however, also the addition of the crowding agent Ficoll destabilized the dimer while the addition of bovine serum albumin (BSA) and lysozyme, often used to represent interaction with charged macromolecules, had no effect. Our results highlight the potential of DEER for in-cell study of proteins as well as the complexities of the effects of the cellular milieu on protein structures and stability.

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48

Höfig, Henning, Michele Cerminara, Ilona Ritter, Antonie Schöne, Martina Pohl, Victoria Steffen, Julia Walter, Ignacio Vergara Dal Pont, Alexandros Katranidis, and Jörg Fitter. "Single-Molecule Studies on a FRET Biosensor: Lessons from a Comparison of Fluorescent Protein Equipped versus Dye-Labeled Species." Molecules 23, no. 12 (November 27, 2018): 3105. http://dx.doi.org/10.3390/molecules23123105.

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Bacterial periplasmic binding proteins (PBPs) undergo a pronounced ligand-induced conformational change which can be employed to monitor ligand concentrations. The most common strategy to take advantage of this conformational change for a biosensor design is to use a Förster resonance energy transfer (FRET) signal. This can be achieved by attaching either two fluorescent proteins (FPs) or two organic fluorescent dyes of different colors to the PBPs in order to obtain an optical readout signal which is closely related to the ligand concentration. In this study we compare a FP-equipped and a dye-labeled version of the glucose/galactose binding protein MglB at the single-molecule level. The comparison demonstrates that changes in the FRET signal upon glucose binding are more pronounced for the FP-equipped sensor construct as compared to the dye-labeled analog. Moreover, the FP-equipped sensor showed a strong increase of the FRET signal under crowding conditions whereas the dye-labeled sensor was not influenced by crowding. The choice of a labeling scheme should therefore be made depending on the application of a FRET-based sensor.

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49

Yu, Isseki, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, and Michael Feig. "Dynamics and Interactions of Proteins and Metabolites in Cellular Crowding Environments: All-Atom Molecular Dynamics Study of Proteins and Metabolites in Cellular Crowding Environments: All-atom Molecular Dynamics Study." Biophysical Journal 114, no. 3 (February 2018): 190a. http://dx.doi.org/10.1016/j.bpj.2017.11.1063.

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50

Madden, T. L., and J. Herzfeld. "Crowding-induced organization of cytoskeletal elements: II. Dissolution of spontaneously formed filament bundles by capping proteins." Journal of Cell Biology 126, no. 1 (July 1, 1994): 169–74. http://dx.doi.org/10.1083/jcb.126.1.169.

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Through calculations of molecular packing constraints in crowded solutions, we have previously shown that dispersions of filament forming proteins and soluble proteins can be unstable at physiological concentrations, such that tight bundles of filaments are formed spontaneously, in the absence of any accessory binding proteins. Here we consider the modulation of this phenomenon by capping proteins. The theory predicts that, by shortening the average filament length, capping alleviates the packing problem. As a result, the dispersed isotropic solution is stable over an expanded range of compositions.

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