Relevant bibliographies by topics / Macromolecular crowding agents

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  2. Dissertations / Theses
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Academic literature on the topic 'Macromolecular crowding agents'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Macromolecular crowding agents"

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De Pieri, Andrea, Shubhasmin Rana, Stefanie Korntner, and Dimitrios I. Zeugolis. "Seaweed polysaccharides as macromolecular crowding agents." International Journal of Biological Macromolecules 164 (December 2020): 434–46. http://dx.doi.org/10.1016/j.ijbiomac.2020.07.087.

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Lee, Hong Bok, Anh Cong, Hannah Leopold, Megan Currie, Arnold J. Boersma, Erin D. Sheets, and Ahmed A. Heikal. "Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments." Physical Chemistry Chemical Physics 20, no. 37 (2018): 24045–57. http://dx.doi.org/10.1039/c8cp03873b.

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Stepanenko, Olesya V., Olga V. Stepanenko, Irina M. Kuznetsova, and Konstantin K. Turoverov. "The unfolding of iRFP713 in a crowded milieu." PeerJ 7 (April 8, 2019): e6707. http://dx.doi.org/10.7717/peerj.6707.

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The exploring of biological processes in vitro under conditions of macromolecular crowding is a way to achieve an understanding of how these processes occur in vivo. In this work, we study the unfolding of the fluorescent probe iRFP713 in crowded environment in vitro. Previously, we showed that the unfolding of the dimeric iRFP713 is accompanied by the formation of a compact monomer and an intermediate state of the protein. In the intermediate state, the macromolecules of iRFP713 have hydrophobic clusters exposed to the surface of the protein and are prone to aggregation. Concentrated solutions of polyethylene glycol (PEG-8000), Dextran-40 and Dextran-70 with a molecular mass of 8000, 40000 and 70000 Da, respectively, were used to model the conditions for macromolecular crowding. A limited available space provided by all the crowding agents used favors to the enhanced aggregation of iRFP713 in the intermediate state at the concentration of guanidine hydrochloride (GdnHCl), at which the charge of protein surface is neutralized by the guanidine cations. This is in line with the theory of the excluded volume. In concentrated solutions of the crowding agents (240–300 mg/ml), the stabilization of the structure of iRFP713 in the intermediate state is observed. PEG-8000 also enhances the stability of iRFP713 in the monomeric compact state, whereas in concentrated solutions of Dextran-40 and Dextran-70 the resistance of the protein in the monomeric state against GdnHCl-induced unfolding decreases. The obtained data argues for the excluded volume effect being not the only factor that contributes the behavior of biological molecules in a crowded milieu. Crowding agents do not affect the structure of the native dimer of iRFP713, which excludes the direct interactions between the target protein and the crowding agents. PEGs of different molecular mass and Dextran-40/Dextran-70 are known to influence the solvent properties of water. The solvent dipolarity/polarizability and basicity/acidity in aqueous solutions of these crowding agents vary in different ways. The change of the solvent properties in aqueous solutions of crowding agents might impact the functioning of a target protein.
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del Álamo, Marta, Germán Rivas, and Mauricio G. Mateu. "Effect of Macromolecular Crowding Agents on Human Immunodeficiency Virus Type 1 Capsid Protein Assembly In Vitro." Journal of Virology 79, no. 22 (November 15, 2005): 14271–81. http://dx.doi.org/10.1128/jvi.79.22.14271-14281.2005.

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ABSTRACT Previous studies on the self-assembly of capsid protein CA of human immunodeficiency virus type 1 (HIV-1) in vitro have provided important insights on the structure and assembly of the mature HIV-1 capsid. However, CA polymerization in vitro was previously observed to occur only at very high ionic strength. Here, we have analyzed the effects on CA assembly in vitro of adding unrelated, inert macromolecules (crowding agents), aimed at mimicking the crowded (very high macromolecular effective concentration) environment within the HIV-1 virion. Crowding agents induced fast and efficient polymerization of CA even at low (close to physiological) ionic strength. The hollow cylinders thus assembled were indistinguishable in shape and dimensions from those formed in dilute protein solutions at high ionic strength. However, two important differences were noted: (i) disassembly by dilution of the capsid-like particles was undetectable at very high ionic strength, but occurred rapidly at low ionic strength in the presence of a crowding agent, and (ii) a variant CA from a presumed infectious HIV-1 with mutations at the CA dimerization interface was unable to assemble at any ionic strength in the absence of a crowding agent; in contrast, this mutation allowed efficient assembly, even at low ionic strength, when a crowding agent was used. The use of a low ionic strength and inert macromolecules to mimic the crowded environment inside the HIV-1 virion may lead to a better in vitro evaluation of the effects of conditions, mutations or/and other molecules, including potential antiviral compounds, on HIV-1 capsid assembly, stability and disassembly.
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Gnutt, David, and Simon Ebbinghaus. "The macromolecular crowding effect – from in vitro into the cell." Biological Chemistry 397, no. 1 (January 1, 2016): 37–44. http://dx.doi.org/10.1515/hsz-2015-0161.

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Abstract The influence of the cellular milieu, a complex and crowded solvent, is often neglected when biomolecular structure and function are studied in vitro. To mimic the cellular environment, crowding effects are commonly induced in vitro using artificial crowding agents like Ficoll or dextran. However, it is unclear if such effects are also observed in cellulo. Diverging results on protein stability in living cells point out the need for new quantitative methods to investigate the contributions of excluded volume and nonspecific interactions to the cellular crowding effect. We show how new crowding sensitive probes may be utilized to directly investigate crowding effects in living cells. Moreover, we discuss processes where crowding effects could play a crucial role in molecular cell biology.
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Vweza, Alick-O., Chul-Gyu Song, and Kil-To Chong. "Liquid–Liquid Phase Separation in the Presence of Macromolecular Crowding and State-Dependent Kinetics." International Journal of Molecular Sciences 22, no. 13 (June 22, 2021): 6675. http://dx.doi.org/10.3390/ijms22136675.

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Biomolecular condensates formed via liquid–liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn–Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.
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Zhou, Huan-Xiang. "Effect of mixed macromolecular crowding agents on protein folding." Proteins: Structure, Function, and Bioinformatics 72, no. 4 (May 27, 2008): 1109–13. http://dx.doi.org/10.1002/prot.22111.

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Biswas, Saikat, and Pramit K. Chowdhury. "Unusual domain movement in a multidomain protein in the presence of macromolecular crowders." Physical Chemistry Chemical Physics 17, no. 30 (2015): 19820–33. http://dx.doi.org/10.1039/c5cp02674a.

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Zhang, Chen, Fang Li, Si-Xi Wang, Zhao-Sheng Liu, and Haji Akber Aisa. "Molecularly imprinted polymers prepared using a porogenic solvent of an ionic liquid and a macromolecular crowding agent and their application in purification of oleanic acid." Analytical Methods 7, no. 24 (2015): 10256–65. http://dx.doi.org/10.1039/c5ay01960e.

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A strategy to increase the affinity of molecularly imprinted polymers (MIPs) using a novel porogenic solvent was described based on the cooperative effect of ionic liquids and macromolecular crowding agents.
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Koch, Leon, Roland Pollak, Simon Ebbinghaus, and Klaus Huber. "A Comparative Study on Cyanine Dyestuffs as Sensor Candidates for Macromolecular Crowding In Vitro and In Vivo." Biosensors 13, no. 7 (July 8, 2023): 720. http://dx.doi.org/10.3390/bios13070720.

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Pseudo isocyanine chloride (PIC) has been identified in a preceding work as a sensor suited to probe macromolecular crowding both in test tubes with solutions of synthetic crowding agents and in HeLa cells as a representative of living systems. The sensing is based on a delicate response of the self-assembly pattern of PIC towards a variation in macromolecular crowding. Based on a suitable selection of criteria established in the present study, four additional cyanine dyestuffs (TDBC, S071, S2275, and PCYN) were scrutinized for their ability to act as such a sensor, and the results were compared with the corresponding performance of PIC. UV-VIS and fluorescence spectroscopy were applied to investigate the photo-physical properties of the four candidates and, if possible, light scattering was used to characterize the self-assembly of the dyestuffs in solution. Finally, HeLa cells were exposed to solutions of the most promising candidates in order to analyze their ability to infiltrate the cells and to self-assemble therein. None of the dyestuff candidates turned out to be as similarly promising in probing crowding effects in cells as PIC turned out to be. S0271 and S2275 are at least stable enough and meet the photophysical requirements necessary to act as sensors responding to changes in macromolecular crowding.
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Dissertations / Theses on the topic "Macromolecular crowding agents"

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Cooper, Elisa. "[alpha]-synuclein oligomer formation and the effect of macromolecular crowding agents on fibrillation /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2005. http://uclibs.org/PID/11984.

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Kundu, Jayanta. "Study of heme proteins in presence of macromolecular crowding agents." Thesis, 2017. http://localhost:8080/iit/handle/2074/7458.

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Hsu, Yun-Hsiang, and 許雲翔. "The effect of hydrophilicity on macromolecular crowding in paramagnetic solution of magnetic resonance imaging contrast agent." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/13025929986776183900.

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碩士
國立中山大學
化學系研究所
102
The power of MRI is tremendously enhanced by the application of various types of MRI contrast agents which increase the relaxivity of water molecules close to them through strong dipolar interactions between water and the paramagnetic ions on the contrast agent. With about 30 years of advancement, MRI contrast agents with various functions, such as signal enhancement, target selection and molecular or event specificity, have been developed. More MRI contrast agents with different purposes are under development today. To better understand the mechanism of MRI contrast agents in various conditions and to develop new generation MRI contrast agents, it is desired that the interactions between the MRI contrast agents and other molecules in their proximity are better understood. We have found that macromolecular crowding effect is an important contributing factor that affects the performance of MRI contrast agents. Therefore, we have decided to carry out a full investigation of this phenomenon with different crowding molecules and MRI contrast agents. This work will report the results with sodium polyacrylate (NaPA) as crowder and Dotarem as MRI contrast agent and focus on the hydrophiliity of macromolecules. A linear relationship is found between the concentration of Dotarem and relaxation rates and chemical shift. A nonlinear relationship is found between the concentration of NaPA and relaxation rates and chemical shift. The hydrophilicity of macromolecular crowders has significant influence on overall crowding effect. The simple picture of volume exclusion must be updated and intermolecular interactions must be taken into account. Morevoer, the details of the crowding effect of NaPA and that of PEG are compared and discussed.
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Hsin, Yu-Chun, and 忻佑純. "The Crowding Effect of Ficoll 70 on Magnetic Resonance Imaging Contrast Agent Dotarem and Comparison with Other Macromolecular Crowders." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/27473276712915148733.

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碩士
國立中山大學
化學系研究所
102
Owing to its many advantages such as noninvasiveness and its ability for providing multiple layers of information on structure and dynamics, magnetic resonance imaging (MRI) has become an essential clinical equipment but also a powerful tool for basic research in various fields. By using MRI contrast agents, more specificity and selectivity can be achieved with MRI, which has prompted the development of thousands of MRI contrast agents over the past decades. The performance of the MRI contrast agent depends on their chemical structure and the interaction with the other molecules around them such as water. The basic principle of MRI contrast agents is to increase water relaxation with paramagnetic ions. The performance of an MRI contrast agent depends not only on the structure and dynamics of the compound, but also on the environment it is located. In a typical living system, there are lots of macromolecules such as proteins, lipids, sugars, nucleic acids, ribosomes etc, making cell a highly crowded environment. To obtain insight into the influence of water motions by Dotarem under the crowded conditions, we use three types of crowding agent (Ficoll 70、NaPA、PEG6000). Ficoll 70 (70 kDa) is a synthetic crowding agent and a cross-linked sucrose polymer. NaPA and PEG6000 are linear structural polymers. We used nuclear magnetic resonance spectroscopy (NMR) to measure the longitudinal relaxation rate (R1), transverse relaxation rate (R2), translational diffusion, MRI and NMRD (Nuclear Magnetic Relaxation Dispersion) under different concentrations of crowders and contrast agent. We have found that macromolecular crowding effect is an important contributing factor that affects the performance of MRI contrast agents. The details of the crowding effect of different crowding agents are compared and discussed. The results demonstrate the significant effect of crowders on the relaxivity of MRI contrast agent and indicate that a molecular level understanding of the relaxtion mechanism of MRI contrast agent in a crowded environment helps establishment of a microscopic picture of MRI contrast generation and prevents mistakes in diagnosis in medical MRI.
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Chen, Shou-fu, and 陳碩甫. "NMR diffusion and relaxation reveal significant ionic influence and macromolecular crowding effect on the performance of magnetic resonance imaging contrast agent." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/11265763746210448015.

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Abstract:
碩士
國立中山大學
化學系研究所
104
Magnetic resonance imaging (MRI) has become the most important non-invasive method for providing three dimensional detailed images without using damaging radiation and is a powerful tool in materials science, biomedicine, medical diagnosis, food science and many other fields. In many situations such as in disease detection, however, the image contrast is not sufficient. Therefore, through the MRI contrast agent, its high paramagnetic ion can effectively and selectively accelerate water 1H nuclear relaxation rates. Therefore, water molecules in different microenvironments obtain a different relaxation acceleration so that a better contrast is achieved for the diseased regions. However, current theory for MRI contrast agent was developed by assuming that the paramagnetic ions are located in a dilute aqueous solution. This is a good approximation in many situations such as water in a relatively free microenvironments, but cellular environment is highly crowded with various kinds of biomacromolecules (proteins, hydrocarbonates, genetic materials etc), small molecules (hormones, vitamins etc) and ions (H+, Na+, K+, Cl- etc). The performance of MRI contrast agent may be significantly altered by crowders and ions. Understanding how the contrast agent interacts with other molecules in cell is a very important and challenging problem. In this work, we focus on the influence of common ions in organisms and macromolecular crowding effect on the performance of MRI contrast agent. The MRI contrast agent we chose is Dotarem which is the mostly used in medical diagnosis.. Then we follow the standard practice of selecting a macromolecular crowder (polyethylene glycol, M.W. 6000, PEG6k, an artificial inert macromolecule, with no specific structure in aqueous solutions) to mimic cellular environment. The ions used here are those mostly commonly found in humans (LiCl, NaCl, KCl, MgCl2, CaCl2, NaI). 1H NMR relaxation rates and translational diffusion rate of water and PEG6k are measured on a 500 MHz NMR spectrometer equipped with a Pulse Filed Gradient (PFG) unit. It is found that the longitudinal relaxation rates and translational diffusion coefficient are sensitive measures for quantifying the effects of ions and macromolecular crowders on the performance of MRI contrast agent. Within the concentration range typically present in an organism, these dynamic parameters are found to clearly depend on the concentration, type and valence number of the ions besides the concentration of MRI contrast agent and macromolecular crowding effect. These results are further supplemented by fast field cycling relaxometry (NMR relaxation dispersion) over a range between 0.01 – 40 MHz. The physical chemistry mechanism of these effects is elucidated by analyzing the experimental results. The significance of these effects to practical MRI is discussed. Based on the experimental and theoretical results as well as the analysis, we conclude that both the ionic and macromolecular effects must be taken into account for more precise MRI diagnosis or functional MRI studies.
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Book chapters on the topic "Macromolecular crowding agents"

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Reddy, Michael K., Stephen E. Weitzel, Shirley S. Daube, Thale C. Jarvis, and Peter H. von Hippel. "[36] Using macromolecular crowding agents to identify weak interactions within DNA replication complexes." In Methods in Enzymology, 466–76. Elsevier, 1995. http://dx.doi.org/10.1016/0076-6879(95)62038-9.

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