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Löwe M, Hänsch S, Hachani E, Schmitt L, Weidtkamp-Peters S, Kedrov A. Probing macromolecular crowding at the lipid membrane interface with genetically-encoded sensors. Protein Sci 2023; 32:e4797. [PMID: 37779215 PMCID: PMC10578116 DOI: 10.1002/pro.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein-packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non-invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically-encoded fluorescence-based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane-tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding-dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis.
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Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Hänsch
- Center for Advanced imaging, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eymen Hachani
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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2
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Bai Q, Chen X, Chen J, Liu Z, Lin YN, Yang S, Liang D. Morphology and Dynamics of Coexisting Phases in Coacervate Solely Controlled by Crowded Environment. ACS Macro Lett 2022; 11:1107-1111. [PMID: 36006377 DOI: 10.1021/acsmacrolett.2c00409] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The membraneless organelles (MLOs) play a key role in the cell, yet it is unclear what controls the morphology and dynamics of MLOs in crowded cell medium. Using a biphasic coacervate droplet as a model of MLO, we online monitored the liquid-liquid phase separation process in crowded medium provided by poly(ethylene oxide) (PEO) or dextran. In PEO solution, which has an affinity with the inner phase, the spherical droplets evolve into clusters, networks, and completely phase inverted spheres in sequence with increasing PEO concentration, while in dextran solution, which has an affinity with the outer phase, the coacervates maintain the morphology but vary in phase ratio. Flower-like and even Janus structures are formed in the mixed PEO/dextran medium. Our work demonstrates that MLOs could be controlled solely by the crowded cell medium.
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Affiliation(s)
- Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ya-Nan Lin
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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3
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Majumdar BB, Mondal J. Impact of Inert Crowders on Host-Guest Recognition Process. J Phys Chem B 2022; 126:4200-4215. [PMID: 35654414 DOI: 10.1021/acs.jpcb.2c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological environments typically contain high concentrations (300-400 mg/mL) of different macromolecules at volume fractions as large as 30%-40%. Biomolecular recognition processes, a ubiquitous biological phenomena, occurring in such crowded heterogeneous media would differ significantly compared to the dilute buffer solutions. Here we quantify the potential impact of inert crowders on prototypical host-guest recognition process by explicit-solvent molecular dynamics (MD) simulations in atomic resolution. We demonstrate that the crowders, when smaller in size, would facilitate the binding process of the guest molecule by decreasing the free energy barrier for binding via excluded volume effect and desolvation of the host receptor. However, the extent of crowder-induced stabilization of a host-guest complex is found to be significantly higher when the guest molecule is sterically constricted to approach the host along a centrosymmetric direction, compared to its unrestricted, freely diffusive movement. A kinetic analysis of the recognition process reveals that the origin of a relatively stronger crowder impact during constricted movement of guest molecule lies in the relatively enhanced residence time of the guest inside the host by crowders. Together, our results suggest that the extent of impact of crowding on recognition processes would be contingent upon the presence or absence of constriction on ligand movement.
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A modified protocol with less clean-up steps increased efficiency and product yield of sequencing library preparation. 3 Biotech 2022; 12:111. [PMID: 35462954 PMCID: PMC8995211 DOI: 10.1007/s13205-022-03168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/19/2022] [Indexed: 11/01/2022] Open
Abstract
Library preparation is an essential step for the next-generation sequencing, such as whole-genome sequencing, reduced-representation genome sequencing, exome sequencing and transcriptome sequencing. The library preparation often involves many steps, including DNA fragmentation, end repair, ligation and amplification. Each step involves different enzymes and buffer systems, so many washing steps are implemented in between to clean-up the enzymes and solutes from the previous step. Those extra washing steps not only are tedious and costly, but more importantly may introduce cross-contamination and reduce the final library yield. Here, we modified the common protocol of Illumina library prep to reduce the washing steps by deactivating the enzymes with high temperature. The modified protocol has two less washing steps than the original one, which can save more than 40 min of hands-on time and reduce potential risk of cross-contamination. We compared our protocol with the original one by constructing libraries using 200 ng DNA of Tetraodon nigroviridis. The results showed that libraries prepared with the modified protocol had higher yields than that using the original protocol (53.4 ± 16.8 ng/ml vs. 8 ± 0.7 ng/ml), whereas the coverage and PCR duplication rate were similar. Furthermore, we eliminated the very first washing step after DNA shearing to preserve short DNA fragments, which increased proportion of fragments less than 100 bp DNA from 0.82 to 2.99%. In conclusion, using the modified protocols not only can save time and money, but also can generate higher yield and keep more short DNA fragments. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03168-5.
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Bilotti K, Potapov V, Pryor JM, Duckworth AT, Keck J, Lohman GJS. OUP accepted manuscript. Nucleic Acids Res 2022; 50:4647-4658. [PMID: 35438779 PMCID: PMC9071435 DOI: 10.1093/nar/gkac241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/07/2022] [Accepted: 03/31/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - John M Pryor
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Gregory J S Lohman
- To whom correspondence should be addressed. Tel: +1 978 998 7916; Fax: +1 978 921 1350;
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Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 2021; 184:6174-6192.e32. [PMID: 34813726 PMCID: PMC8671326 DOI: 10.1016/j.cell.2021.10.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.
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Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nat Commun 2021; 12:4099. [PMID: 34215742 PMCID: PMC8253829 DOI: 10.1038/s41467-021-24349-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
The inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1), in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase.
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8
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It is time to crowd your cell culture media - Physicochemical considerations with biological consequences. Biomaterials 2021; 275:120943. [PMID: 34139505 DOI: 10.1016/j.biomaterials.2021.120943] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
In vivo, the interior and exterior of cells is populated by various macromolecules that create an extremely crowded milieu. Yet again, in vitro eukaryotic cell culture is conducted in dilute culture media that hardly imitate the native tissue density. Herein, the concept of macromolecular crowding is discussed in both intracellular and extracellular context. Particular emphasis is given on how the physicochemical properties of the crowding molecules govern and determine kinetics, equilibria and mechanism of action of biochemical and biological reactions, processes and functions. It is evidenced that we are still at the beginning of appreciating, let alone effectively implementing, the potential of macromolecular crowding in permanently differentiated and stem cell culture systems.
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Mondal S, Mishra PP. Direct observation of effect of crowding induced macromolecular hydration on molecular breathing in the stem of Fork-DNA by single-molecule FRET microspectroscopy. Int J Biol Macromol 2020; 167:559-569. [PMID: 33278436 DOI: 10.1016/j.ijbiomac.2020.11.197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/15/2022]
Abstract
The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.
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Affiliation(s)
- Soma Mondal
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
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10
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Williamson A, Leiros HKS. Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res 2020; 48:8225-8242. [PMID: 32365176 PMCID: PMC7470946 DOI: 10.1093/nar/gkaa307] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
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Affiliation(s)
- Adele Williamson
- School of Science, University of Waikato, Hamilton 3240, New Zealand.,Department of Chemistry, UiT The Arctic University of Norway, Tromsø N-9037, Norway
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11
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Mechanistic investigation of bead-based padlock rolling circle amplification under molecular crowding conditions. Anal Biochem 2020; 593:113596. [DOI: 10.1016/j.ab.2020.113596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022]
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Ogunmoyole T, Adewale IO, Fodeke AA, Afolayan A. Catalytic studies of glutathione transferase from Clarias gariepinus (Burchell) in dilute and crowded solutions. Comp Biochem Physiol C Toxicol Pharmacol 2020; 228:108648. [PMID: 31672530 DOI: 10.1016/j.cbpc.2019.108648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
Abstract
Kinetic properties of purified Clarias gariepinus glutathione transferase (CgGST) was studied in the presence of Ficoll 70, Polyethylene glycol (PEG) 6000, bovine serum albumin (BSA) and in dilute solution. This was done to mimic the cytosol thereby unraveling the actual mechanism of detoxication involving glutathione transferase (GST) in the crowded intracellular milieu. CgGST from the liver of Clarias gariepinus was purified to homogeneity by affinity chromatography on glutathione (GSH) - agarose. Initial-velocity study was performed by varying the concentrations of GSH at various fixed concentrations of 1-chloro-2,4-dinitrobenzene (CDNB) and vice-versa. Data obtained were fitted to the three equations representing random-ordered, compulsory-ordered and ping-pong mechanisms to obtain kinetic parameters. Product inhibition studies using sodium chloride (NaCl) was done by varying the concentrations of NaCl and CDNB at a fixed concentration of GSH and vice-versa. Data obtained were fitted to three equations representing competitive, non-competitive and uncompetitive inhibitions to obtain the inhibition constants (KiGSH and KiCDNB). Optimal temperature of CgGST activity was 20 °C both in dilute and crowded solutions. Maximum velocity (Vmax) in dilute solution was decreased, while KmGSH and KmCDNB were increased in the presence of the crowding agents. Turnover number (kcat), catalytic efficiency - kcat/KmGSH,kcat/KmCDNB and inhibition constants - (KiGSH and KiCDNB) were reduced in crowded solutions. Mechanism of catalysis was steady - state random sequential in both dilute and crowded solutions. The study concluded that although the catalytic efficiency of the enzyme was reduced in crowded solution, mechanism of catalysis remains the same in both crowded and dilute solutions.
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Affiliation(s)
- Temidayo Ogunmoyole
- Department of Medical Biochemistry, College of Medicine, Ekiti State University, Ado-Ekiti, Nigeria.
| | - Isaac Olusanjo Adewale
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife 220282, Nigeria.
| | - Adedayo A Fodeke
- Department of Chemistry, Obafemi Awolowo, University, Ile-Ife 220282, Nigeria
| | - Adeyinka Afolayan
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife 220282, Nigeria
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13
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Abstract
DNA ligases are used chiefly to create novel combinations of nucleic acid molecules and to attach them to vectors before molecular cloning. They are either of bacterial origin or bacteriophage encoded and have different properties, as discussed here.
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14
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Murade CU, Shubeita GT. A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm. ACS Sens 2019; 4:1835-1843. [PMID: 31250628 DOI: 10.1021/acssensors.9b00569] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We describe a molecular sensor that reports, using fluorescence resonance energy transfer (FRET), on the degree of macromolecular crowding in different cellular compartments. The oligonucleotide-based sensor is sensitive to changes in the volume fraction of macromolecules over a wide range in vitro and, when introduced in cells, rapidly distributes and shows a striking contrast between the cytosol and the nucleus. This contrast can be modulated by osmotic stress or by using a number of drugs that alter chromatin organization within the nucleus. These findings suggest that the sensor can be used as a tool to probe chromosome organization. Further, our finding that the cell maintains different degrees of macromolecular crowding in the cytoplasm and nucleoplasm has implications on molecular mechanisms since crowding can alter protein conformations, binding rates, reaction kinetics, and therefore protein function.
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Affiliation(s)
- Chandrashekhar U. Murade
- Physics Program, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - George T. Shubeita
- Physics Program, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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15
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Scott S, Shaheen C, McGuinness B, Metera K, Kouzine F, Levens D, Benham CJ, Leslie S. Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules. Nucleic Acids Res 2019; 47:6360-6368. [PMID: 31106378 PMCID: PMC6614806 DOI: 10.1093/nar/gkz408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
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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Affiliation(s)
- Shane Scott
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Cynthia Shaheen
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Brendon McGuinness
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MS 20892, USA
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MS 20892, USA
| | - Craig J Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina Leslie
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
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16
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Maximova K, Wojtczak J, Trylska J. Enzyme kinetics in crowded solutions from isothermal titration calorimetry. Anal Biochem 2018; 567:96-105. [PMID: 30439369 DOI: 10.1016/j.ab.2018.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/08/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Isothermal titration calorimetry (ITC) is a universal technique that directly measures the heat absorbed or released in a process. ITC is typically used to determine thermodynamic parameters of association of molecules without the need to label them. However, ITC is still rarely applied to study chemical reactions catalyzed by enzymes. In addition, these few studies of enzyme kinetic measurements that have been performed were in diluted solutions. Yet, to estimate realistic kinetic parameters, we have to account for the fact that enzymatic reactions in cells occur in a crowded environment because cells contain 200-400 g/L of macromolecular crowders such as proteins, ribosomes and lipids. Thus we expanded the ITC application for solutions mimicking the cellular environment by adding various macromolecular crowders. We investigated how these crowders affect the kinetics of trypsin-catalyzed reactions and determined the Michaelis-Menten parameters for hydrolysis of two trypsin substrates: Nα-benzoyl-l-arginine ethyl ester (BAEE) and Nα-benzoyl-dl-arginine β-naphthylamide (BANA). Since ITC enables investigations of complex and turbid solutions with label-free reagents, it seems a perfect technique for kinetic analyses in crowded solutions. ITC also offers the opportunity to control enzyme-crowder and substrate-crowder interactions.
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Affiliation(s)
- Ksenia Maximova
- Centre of New Technologies University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
| | - Jakub Wojtczak
- Centre of New Technologies University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland; Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warszawa, Poland
| | - Joanna Trylska
- Centre of New Technologies University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
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17
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Extracellular fluid viscosity enhances liver cancer cell mechanosensing and migration. Biomaterials 2018; 177:113-124. [DOI: 10.1016/j.biomaterials.2018.05.058] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Accepted: 05/31/2018] [Indexed: 12/31/2022]
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18
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Bagnoli JW, Ziegenhain C, Janjic A, Wange LE, Vieth B, Parekh S, Geuder J, Hellmann I, Enard W. Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nat Commun 2018; 9:2937. [PMID: 30050112 PMCID: PMC6062574 DOI: 10.1038/s41467-018-05347-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to develop a scRNA-seq library protocol we call molecular crowding SCRB-seq (mcSCRB-seq), which we show to be one of the most sensitive, efficient, and flexible scRNA-seq methods to date.
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Affiliation(s)
- Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
- Department of Cell & Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Aleksandar Janjic
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany.
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Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun (Camb) 2018; 54:6408-6411. [PMID: 29872779 DOI: 10.1039/c8cc02414f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 box 1041, 3000 Leuven, Belgium.
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20
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Crowded milieu tuning the stability and activity of stem bromelain. Int J Biol Macromol 2018; 109:114-123. [DOI: 10.1016/j.ijbiomac.2017.12.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 11/24/2022]
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21
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Singh P, Choudhury S, Dutta S, Adhikari A, Bhattacharya S, Pal D, Pal SK. Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding. Int J Biol Macromol 2017; 103:395-402. [DOI: 10.1016/j.ijbiomac.2017.05.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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22
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Brudzynski K, Miotto D, Kim L, Sjaarda C, Maldonado-Alvarez L, Fukś H. Active macromolecules of honey form colloidal particles essential for honey antibacterial activity and hydrogen peroxide production. Sci Rep 2017; 7:7637. [PMID: 28794506 PMCID: PMC5550472 DOI: 10.1038/s41598-017-08072-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/30/2017] [Indexed: 11/09/2022] Open
Abstract
Little is known about the global structure of honey and the arrangement of its main macromolecules. We hypothesized that the conditions in ripened honeys resemble macromolecular crowding in the cell and affect the concentration, reactivity, and conformation of honey macromolecules. Combined results from UV spectroscopy, DLS and SEM showed that the concentration of macromolecules was a determining factor in honey structure. The UV spectral scans in 200-400 nm visualized and allowed quantification of UV-absorbing compounds in the following order: dark > medium > light honeys (p < 0.0001). The high concentration of macromolecules promoted their self-assembly to micron-size superstructures, visible in SEM as two-phase system consisting of dense globules distributed in sugar solution. These particles showed increased conformational stability upon dilution. At the threshold concentration, the system underwent phase transition with concomitant fragmentation of large micron-size particles to nanoparticles in hierarchical order. Honey two-phase conformation was an essential requirement for antibacterial activity and hydrogen peroxide production. These activities disappeared beyond the phase transition point. The realization that active macromolecules of honey are arranged into compact, stable multicomponent assemblies with colloidal properties reframes our view on global structure of honey and emerges as a key property to be considered in investigating its biological activity.
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Affiliation(s)
- Katrina Brudzynski
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada.
| | - Danielle Miotto
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Linda Kim
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Calvin Sjaarda
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Liset Maldonado-Alvarez
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
| | - Henryk Fukś
- Department of Mathematics & Statistics, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada
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23
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Molecular crowding improves bead-based padlock rolling circle amplification. Anal Biochem 2017; 519:15-18. [DOI: 10.1016/j.ab.2016.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 11/21/2022]
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24
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Rao A, Cölfen H. On the biophysical regulation of mineral growth: Standing out from the crowd. J Struct Biol 2016; 196:232-243. [DOI: 10.1016/j.jsb.2016.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
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25
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Suzuki M, Hayashi H, Mizuki T, Maekawa T, Morimoto H. Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field. Biochem Biophys Rep 2016; 8:360-364. [PMID: 28955977 PMCID: PMC5614472 DOI: 10.1016/j.bbrep.2016.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 07/20/2016] [Accepted: 10/10/2016] [Indexed: 12/02/2022] Open
Abstract
We present a simple method for efficient DNA ligation utilizing the heat generation of ferromagnetic particles subjected to an ac magnetic field. We carry out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on the surface of ferromagnetic particles. When a radio frequency alternating magnetic field is applied, ferromagnetic particles dissipate heat and DNA ligase on the particles is selectively heated up and activated with little influence on the annealing of DNA ends, as a result of which the ligation efficiency increases. We show that the ligation efficiency increases with an increase in the field amplitude. DNA ligation is performed with T4 DNA ligase immobilized on iron particles. Heat generation of iron particles in an ac magnetic field promotes DNA ligation. The ligation efficiency increases with an increase in the magnetic field amplitude.
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Affiliation(s)
- Masashi Suzuki
- Graduate School of Interdisciplinary New Science, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Hiroaki Hayashi
- Graduate School of Interdisciplinary New Science, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Toru Mizuki
- Graduate School of Interdisciplinary New Science, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan.,Bio-Nano Electronics Research Center, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Toru Maekawa
- Graduate School of Interdisciplinary New Science, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan.,Bio-Nano Electronics Research Center, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Hisao Morimoto
- Graduate School of Interdisciplinary New Science, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan.,Bio-Nano Electronics Research Center, Toyo University, 2100, Kujirai, Kawagoe, Saitama 350-8585, Japan
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26
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Renata H, Lewis RD, Sweredoski MJ, Moradian A, Hess S, Wang ZJ, Arnold FH. Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes. J Am Chem Soc 2016; 138:12527-33. [PMID: 27573353 DOI: 10.1021/jacs.6b06823] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Following the recent discovery that heme proteins can catalyze the cyclopropanation of styrenyl olefins with high efficiency and selectivity, interest in developing new enzymes for a variety of non-natural carbene transfer reactions has burgeoned. The fact that diazo compounds and other carbene precursors are known mechanism-based inhibitors of P450s, however, led us to investigate if they also interfere with this new enzyme function. We present evidence for two inactivation pathways that are operative during cytochrome P450-catalyzed cyclopropanation. Using a combination of UV-vis, mass spectrometry, and proteomic analyses, we show that the heme cofactor and several nucleophilic side chains undergo covalent modification by ethyl diazoacetate (EDA). Substitution of two of the affected residues with less-nucleophilic amino acids led to a more than twofold improvement in cyclopropanation performance (total TTN). Elucidating the inactivation pathways of heme protein-based carbene transfer catalysts should aid in the optimization of this new biocatalytic function.
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Affiliation(s)
- Hans Renata
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Russell D Lewis
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Michael J Sweredoski
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Annie Moradian
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Sonja Hess
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Z Jane Wang
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, MC 210-41, and ‡Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, MC 139-74, California Institute of Technology , 1200 E California Blvd, Pasadena, California 91125, United States
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27
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How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles. Sci Rep 2016; 6:22033. [PMID: 26903405 PMCID: PMC4763241 DOI: 10.1038/srep22033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/04/2016] [Indexed: 12/21/2022] Open
Abstract
In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy.
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28
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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29
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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30
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Li J, Gu L, Aach J, Church GM. Improved cell-free RNA and protein synthesis system. PLoS One 2014; 9:e106232. [PMID: 25180701 PMCID: PMC4152126 DOI: 10.1371/journal.pone.0106232] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/04/2014] [Indexed: 12/13/2022] Open
Abstract
Cell-free RNA and protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant Elements (PURE) system offer new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, protein microarrays, isotopic labeling, and incorporating unnatural amino acids. In this study, using firefly luciferase synthesis as a reporter system, we improved PURE system productivity up to 5 fold by adding or adjusting a variety of factors that affect transcription and translation, including Elongation factors (EF-Ts, EF-Tu, EF-G, and EF4), ribosome recycling factor (RRF), release factors (RF1, RF2, RF3), chaperones (GroEL/ES), BSA and tRNAs. The work provides a more efficient defined in vitro transcription and translation system and a deeper understanding of the factors that limit the whole system efficiency.
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Affiliation(s)
- Jun Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liangcai Gu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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31
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Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 2014; 24:2033-40. [PMID: 25079858 PMCID: PMC4248319 DOI: 10.1101/gr.177881.114] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large-scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from subpicogram amounts of cDNA. The comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, because naked Tn5 can be annealed to any oligonucleotide of choice, for example, molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enable innovation in sequencing-based applications.
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Affiliation(s)
- Simone Picelli
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Asa K Björklund
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Björn Reinius
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Gösta Winberg
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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32
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Gao F, Zhou H, Li W, Zhang X. Detection of ligation products of DNA linkers with 5'-OH ends by denaturing PAGE silver stain. PLoS One 2012; 7:e39251. [PMID: 22761747 PMCID: PMC3384673 DOI: 10.1371/journal.pone.0039251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
To explore if DNA linkers with 5′-hydroxyl (OH) ends could be joined by commercial T4 and E. coli DNA ligase, these linkers were synthesized by using the solid-phase phosphoramidite method and joined by using commercial T4 and E. coli DNA ligases. The ligation products were detected by using denaturing PAGE silver stain and PCR method. About 0.5–1% of linkers A–B and E–F, and 0.13–0.5% of linkers C–D could be joined by T4 DNA ligases. About 0.25–0.77% of linkers A–B and E–F, and 0.06–0.39% of linkers C–D could be joined by E. coli DNA ligases. A 1-base deletion (-G) and a 5-base deletion (-GGAGC) could be found at the ligation junctions of the linkers. But about 80% of the ligation products purified with a PCR product purification kit did not contain these base deletions, meaning that some linkers had been correctly joined by T4 and E. coli DNA ligases. In addition, about 0.025–0.1% of oligo 11 could be phosphorylated by commercial T4 DNA ligase. The phosphorylation products could be increased when the phosphorylation reaction was extended from 1 hr to 2 hrs. We speculated that perhaps the linkers with 5′-OH ends could be joined by T4 or E. coli DNA ligase in 2 different manners: (i) about 0.025–0.1% of linkers could be phosphorylated by commercial T4 DNA ligase, and then these phosphorylated linkers could be joined to the 3′-OH ends of other linkers; and (ii) the linkers could delete one or more nucleotide(s) at their 5′-ends and thereby generated some 5′-phosphate ends, and then these 5′-phosphate ends could be joined to the 3′-OH ends of other linkers at a low efficiency. Our findings may probably indicate that some DNA nicks with 5′-OH ends can be joined by commercial T4 or E. coli DNA ligase even in the absence of PNK.
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Affiliation(s)
- Feng Gao
- Department of Anal and Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huafu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wei Li
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
- * E-mail:
| | - Xuerong Zhang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi, China
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33
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Ge X, Luo D, Xu J. Cell-free protein expression under macromolecular crowding conditions. PLoS One 2011; 6:e28707. [PMID: 22174874 PMCID: PMC3234285 DOI: 10.1371/journal.pone.0028707] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/14/2011] [Indexed: 01/29/2023] Open
Abstract
Background Cell-free protein expression (CFPE) comprised of in vitro transcription and translation is currently manipulated in relatively dilute solutions, in which the macromolecular crowding effects present in living cells are largely ignored. This may not only affect the efficiency of protein synthesis in vitro, but also limit our understanding of the functions and interactions of biomolecules involved in this fundamental biological process. Methodology/Principal Findings Using cell-free synthesis of Renilla luciferase in wheat germ extract as a model system, we investigated the CFPE under macromolecular crowding environments emulated with three different crowding agents: PEG-8000, Ficoll-70 and Ficoll-400, which vary in chemical properties and molecular size. We found that transcription was substantially enhanced in the macromolecular crowding solutions; up to 4-fold increase in the mRNA production was detected in the presence of 20% (w/v) of Ficoll-70. In contrast, translation was generally inhibited by the addition of each of the three crowding agents. This might be due to PEG-induced protein precipitation and non-specific binding of translation factors to Ficoll molecules. We further explored a two-stage CFPE in which transcription and translation was carried out under high then low macromolecular crowding conditions, respectively. It produced 2.2-fold higher protein yield than the coupled CFPE control. The macromolecular crowding effects on CFPE were subsequently confirmed by cell-free synthesis of an approximately two-fold larger protein, Firefly luciferase, under macromolecular crowding environments. Conclusions/Significance Three macromolecular crowding agents used in this research had opposite effects on transcription and translation. The results of this study should aid researchers in their choice of macromolecular crowding agents and shows that two-stage CFPE is more efficient than coupled CFPE.
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Jianfeng Xu
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
- * E-mail:
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34
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Hendrickson CL, Purkayastha S, Pastwa E, Neumann RD, Winters TA. Coincident In Vitro Analysis of DNA-PK-Dependent and -Independent Nonhomologous End Joining. J Nucleic Acids 2010; 2010:823917. [PMID: 20706599 PMCID: PMC2919755 DOI: 10.4061/2010/823917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 06/06/2010] [Indexed: 01/22/2023] Open
Abstract
In mammalian cells, DNA double-strand breaks (DSBs) are primarily repaired by nonhomologous end joining (NHEJ). The current model suggests that the Ku 70/80 heterodimer binds to DSB ends and recruits DNA-PKcs to form the active DNA-dependent protein kinase, DNA-PK. Subsequently, XRCC4, DNA ligase IV, XLF and most likely, other unidentified components participate in the final DSB ligation step. Therefore, DNA-PK plays a key role in NHEJ due to its structural and regulatory functions that mediate DSB end joining. However, recent studies show that additional DNA-PK-independent NHEJ pathways also exist. Unfortunately, the presence of DNA-PKcs appears to inhibit DNA-PK-independent NHEJ, and in vitro analysis of DNA-PK-independent NHEJ in the presence of the DNA-PKcs protein remains problematic. We have developed an in vitro assay that is preferentially active for DNA-PK-independent DSB repair based solely on its reaction conditions, facilitating coincident differential biochemical analysis of the two pathways. The results indicate the biochemically distinct nature of the end-joining mechanisms represented by the DNA-PK-dependent and -independent NHEJ assays as well as functional differences between the two pathways.
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Affiliation(s)
- Cynthia L Hendrickson
- Radiology & Imaging Sciences Department, Nuclear Medicine Section, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
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35
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A QuikChange-like method to realize efficient blunt-ended DNA directional cloning and site-directed mutagenesis simultaneously. Biochem Biophys Res Commun 2010; 397:136-9. [PMID: 20471367 DOI: 10.1016/j.bbrc.2010.05.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 05/10/2010] [Indexed: 11/22/2022]
Abstract
Here we present a QuikChange-like method to efficiently realize blunt-ended DNA cloning and conveniently introduce a site-directed mutation to recombinant plasmid at the same time. After blunt-ended DNA ligation and transformation, the plasmid DNA mixture is extracted from pooled transformants and directly used as template for PCR amplification with a pair of complementary mutagenic primers. With this method, sam1 gene was inserted into pUC19 vector by blunt-end ligation, and a unique restriction site Spe I was introduced to the recombinant plasmid at the same time. The randomly selected transformants were analyzed by DNA sequencing, and most of the clones were found to have correct sequences. However, no correct construct was found from randomly selected transformants after traditional blunt-ended DNA ligation and transformation.
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36
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Tabor S. DNA ligases. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2008; Chapter 3:Unit3.14. [PMID: 18265223 DOI: 10.1002/0471142727.mb0314s08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA ligases catalyze the formation of phosphodiester bonds between juxtaposed 5' phosphate and a 3'-hydroxyl terminus in duplex DNA. This activity can repair single-stranded nicks in duplex DNA and join duplex DNA restriction fragments having either blunt ends or homologous cohesive ends. Two ligases are used for nucleic acid research and their reaction conditions and applications are described in this unit: E. coli ligase and T4 ligase. These enzymes differ in two important properties. One is the source of energy: T4 ligase uses ATP, while E. coli ligase uses NAD. Another important difference is their ability to ligate blunt ends; under normal reaction conditions, only T4 DNA ligase will ligate blunt ends.
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Affiliation(s)
- S Tabor
- Harvard Medical School, Boston, Massachusetts, USA
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37
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Yoshino Y, Ishida M, Horii A. A new 10-min ligation method using a modified buffer system with a very low amount of T4 DNA ligase: the “Coffee Break Ligation” technique. Biotechnol Lett 2007; 29:1557-60. [PMID: 17581703 DOI: 10.1007/s10529-007-9429-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 05/22/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
The ligation reaction is widely used in molecular biology. There are several kits available that complete the ligation reaction very rapidly but they are rather expensive. In this study, we successfully modified the ligation buffer with much lower cost than existing kits. The ligation reaction can be completed in 10 min using very low activities such as 0.01 U T4 DNA ligase, and costs only $1 for 100 reactions of 20 microl scale. We name this ligation system the "Coffee Break Ligation" system; one can complete ligation reaction while drinking a cup of coffee, and perform 100 reactions by spending money equivalent to a cup of coffee.
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Affiliation(s)
- Yuki Yoshino
- Department of Molecular Pathology, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
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38
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Abstract
Here, we examined the effects of molecular crowding on the function, structure and stability of nucleases. We found that the hydrolysis of a 29-mer double-stranded DNA by the endonucleases DNase I and S1 nuclease was substantially enhanced by molecular crowding using polyethylene glycol (PEG); however, molecular crowding had little effect on hydrolysis by exo III and exo I exonucleases. Moreover, kinetic analysis showed that the maximum velocity for the reaction of DNase I at 25°C was increased from 0.1 to 2.7 μM/min by molecular crowding with 20% (w/v) PEG, whereas that of exonuclease I at 37°C decreased from 2.2 to 0.4 μM/min. In contrast, molecular crowding did not significantly affect the Michaelis constant of DNase I or exonuclease I. These results indicate that molecular crowding has different effects on the catalytic activities of exonucleases and endonucleases.
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Affiliation(s)
- Yoshiharu Sasaki
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Fine Co., Ltd., 5-7-8 Shimoshinjo, Higashiyodogawa-ku, Osaka, 533-0021 and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501
| | - Daisuke Miyoshi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Fine Co., Ltd., 5-7-8 Shimoshinjo, Higashiyodogawa-ku, Osaka, 533-0021 and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Fine Co., Ltd., 5-7-8 Shimoshinjo, Higashiyodogawa-ku, Osaka, 533-0021 and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501
- *To whom correspondence should be addressed. +078 435 2497+078 435 2539
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39
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Minsky A, Shimoni E, Englander J. Ring-like nucleoids and DNA repair through error-free nonhomologous end joining in Deinococcus radiodurans. J Bacteriol 2006; 188:6047-51; discussion 6052. [PMID: 16923869 PMCID: PMC1595378 DOI: 10.1128/jb.01951-05] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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40
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Abstract
Live cells contain high concentrations of macromolecules, but almost all experimental biochemical data have been generated from dilute solutions that do not reflect conditions in vivo. To understand biomolecular behavior in vivo, properties studied in vitro are extrapolated to conditions in vivo; however, the molecular conditions within live cells are inherently crowded. The present study investigates the effect of molecular crowding on DNA polymerase activity using polyethylene glycol PEG of various molecular weights as a crowding agent. Polymerase activity assays under various conditions demonstrated that the activities of T7 and Taq DNA polymerases depend on the molecular weight and concentration of the crowding agent. Furthermore, equilibrium and kinetic analyses demonstrated that the binding affinity and catalytic activity of the polymerase increase and decrease, respectively, with increasing PEG concentrations. Based on quantitative parameters of the polymerase reactions, we improved the efficiency of PCR amplification under conditions of molecular crowding. These results suggest that quantitative measurements of biomolecular structure and function are useful for understanding the behavior of biomolecules in vivo and for biotechnology applications in vitro.
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Affiliation(s)
- Yoshiharu Sasaki
- Frontier Institute for Biomolecular Engineering Research FIBER, Konan University, Kobe, Japan
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41
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Abstract
T4 DNA ligase is one of the workhorses of molecular biology and used in various biotechnological applications. Here we report that this ligase, unlike Escherichia coli DNA ligase, Taq DNA ligase and Ampligase, is able to join the ends of single-stranded DNA in the absence of any duplex DNA structure at the ligation site. Such nontemplated ligation of DNA oligomers catalyzed by T4 DNA ligase occurs with a very low yield, as assessed by quantitative competitive PCR, between 10(-6) and 10(-4) at oligonucleotide concentrations in the range 0.1-10 nm, and thus is insignificant in many molecular biological applications of T4 DNA ligase. However, this side reaction may be of paramount importance for diagnostic detection methods that rely on template-dependent or target-dependent DNA probe ligation in combination with amplification techniques, such as PCR or rolling-circle amplification, because it can lead to nonspecific background signals or false positives. Comparison of ligation yields obtained with substrates differing in their strandedness at the terminal segments involved in ligation shows that an acceptor duplex DNA segment bearing a 3'-hydroxy end, but lacking a 5'-phosphate end, is sufficient to play a role as a cofactor in blunt-end ligation.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, MA 02215, USA.
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42
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Wilkinson A, Smith A, Bullard D, Lavesa-Curto M, Sayer H, Bonner A, Hemmings A, Bowater R. Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:113-22. [PMID: 15848142 DOI: 10.1016/j.bbapap.2005.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/03/2005] [Accepted: 03/03/2005] [Indexed: 01/05/2023]
Abstract
NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. NAD(+)-dependent DNA ligases comprise several discrete structural domains, including a BRCT domain at the C-terminus that is highly-conserved in this group of proteins. The over-expression and purification of various fragments of E. coli LigA allowed the investigation of the different domains in DNA-binding and ligation by this enzyme. Compared to the full-length protein, the deletion of the BRCT domain from LigA reduced in vitro ligation activity by 3-fold and also reduced DNA binding. Using an E. coli strain harbouring a temperature-sensitive mutation of ligA, the over-expression of protein with its BRCT domain deleted enabled growth at the non-permissive temperature. In gel-mobility shift experiments, the isolated BRCT domain bound DNA in a stable manner and to a wider range of DNA molecules compared to full LigA. Thus, the BRCT domain of E. coli LigA can bind DNA, but it is not essential for DNA nick-joining activity in vitro or in vivo.
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Affiliation(s)
- Adam Wilkinson
- Phico Therapeutics Ltd, Babraham Hall, Babraham, Cambridge, CB2 4AT, UK
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43
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Hianik T, Rybar P, Andreev SY, Oretskaya TS, Vadgama P. Detection of DNA hybridization on a liposome surface using ultrasound velocimetry and turbidimetry methods. Bioorg Med Chem Lett 2005; 14:3897-900. [PMID: 15225693 DOI: 10.1016/j.bmcl.2004.05.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Revised: 05/21/2004] [Accepted: 05/25/2004] [Indexed: 10/26/2022]
Abstract
19-mer oligonucleotides with oleylamine tethered at 3' and 5' terminal, respectively, were incorporated into unilamellar liposomes of dioleoylphosphatidylcholine (DOPC). Addition of complementary nucleotide resulted in hybridization with oligonucleotides located on different liposomes and caused liposome aggregation. Significant changes of sound velocimetry and turbidity were readily observed at 10 nM concentration of the complementary chain.
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Affiliation(s)
- Tibor Hianik
- Department of Biophysics and Chemical Physics, Comenius University, 842 48 Bratislava, Slovakia.
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44
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Goodrich GP, Helfrich MR, Overberg JJ, Keating CD. Effect of macromolecular crowding on DNA:Au nanoparticle bioconjugate assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:10246-51. [PMID: 15518520 DOI: 10.1021/la048434l] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA:Au nanosphere bioconjugates have applications in biosensing and in the bottom-up assembly of materials. These bioconjugates can be selectively assembled into three-dimensional aggregates upon addition of complementary DNA oligonucleotides and can be dissociated by heating above a melting transition temperature at which the DNA duplexes are denatured. Herein we describe the impact of polymeric solutes on the thermal denaturation behavior of DNA:Au nanoparticle bioconjugate assemblies. Polymeric solutes can dramatically impact biochemical reactions via macromolecular crowding. Poly(ethylene glycol)s (PEGs) and dextrans of varying molecular weights were used as crowding reagents. While both PEG and dextran increased the stability of DNA:Au aggregates, melting transition temperatures in the presence of PEG were impacted more significantly. Polymer molecular weight was less important than polymer chemistry and weight percent in solution. For a high (15%) weight percent of PEG, aggregation was observed even in the absence of complementary oligonucleotides. These results underscore the importance of polymer chemistry in addition to physical volume exclusion in macromolecular crowding and point to the importance of understanding these effects when designing biorecognition-based nanoparticle assembly schemes in complex matrixes (i.e., any involving polymeric solutes).
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Affiliation(s)
- Glenn P Goodrich
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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45
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Lu J, Tong J, Feng H, Huang J, Afonso CL, Rock DL, Barany F, Cao W. Unique ligation properties of eukaryotic NAD+-dependent DNA ligase from Melanoplus sanguinipes entomopoxvirus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1701:37-48. [PMID: 15450174 DOI: 10.1016/j.bbapap.2004.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 05/26/2004] [Accepted: 06/04/2004] [Indexed: 10/26/2022]
Abstract
The eukaryotic Melanoplus sanguinipes entomopoxvirus (MsEPV) genome reveals a homologous sequence to eubacterial nicotinamide adenine dinucleotide (NAD(+))-dependent DNA ligases [J. Virol. 73 (1999) 533]. This 522-amino acid open reading frame (ORF) contains all conserved nucleotidyl transferase motifs but lacks the zinc finger motif and BRCT domain found in conventional eubacterial NAD(+) ligases. Nevertheless, cloned MsEPV ligase seals DNA nicks in a NAD(+)-dependent fashion, while adenosine 5'-monophosphate (ATP) cannot serve as an adenylation cofactor. The ligation activity of MsEPV ligase requires Mg(2+) or Mn(2+). MsEPV ligase seals sticky ends efficiently, but has little activity on 1-nucleotide gap or blunt-ended DNA substrates even in the presence of polyethylene glycol. In comparison, bacterial NAD(+)-dependent ligases seal blunt-ended DNA substrates in the presence of polyethylene glycol. MsEPV DNA ligase readily joins DNA nicks with mismatches at either side of the nick junction, except for mismatches at the nick junction containing an A base in the template strand (A/A, G/A, and C/A). MsEPV NAD(+)-dependent DNA ligase can join DNA probes on RNA templates, a unique property that distinguishes this enzyme from other conventional bacterial NAD(+) DNA ligases. T4 ATP-dependent DNA ligase shows no detectable mismatch ligation at the 3' side of the nick but substantial 5' T/G mismatch ligation on an RNA template. In contrast, MsEPV ligase joins mismatches at the 3' side of the nick more frequently than at the 5' side of the nick on an RNA template. The complementary specificities of these two enzymes suggest alternative primer design for genomic profiling approaches that use allele-specific detection directly from RNA transcripts.
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Affiliation(s)
- Jing Lu
- Department of Genetics, Biochemistry and Life Science Studies, South Carolina Experiment Station, Clemson University, Room 219, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
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46
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Ng PS, Bergstrom DE. Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides. Nucleic Acids Res 2004; 32:e107. [PMID: 15263063 PMCID: PMC506826 DOI: 10.1093/nar/gnh103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 06/25/2004] [Accepted: 06/25/2004] [Indexed: 11/12/2022] Open
Abstract
Oligodeoxyribonucleotides (5'-phosphorylated) of varying lengths were capped using a polyamide linker to form thermodynamically stable, endcapped DNA duplexes containing 8-14 bp. We have employed these endcapped DNA duplexes as tools to determine the DNA footprint of T4 DNA ligase. By high-performance liquid chromatography and PAGE analysis of the ligation mixtures of the endcapped DNA duplexes, we have found that by varying the lengths and the position of the nick, we can determine the minimal DNA-binding site as well as the mode of binding (symmetrical or asymmetrical binding) by the enzyme. The results of the study revealed that a 11 bp endcapped duplex was the shortest duplex effectively ligated. Dependence of ligation efficiency on nick position demonstrates that T4 DNA ligase bound asymmetrically to its DNA substrate. The use of a set of thermodynamically stable endcapped deoxyribonucleoside duplexes as a tool to elucidate the DNA footprint provides an efficient strategy for footprinting, which avoids ambiguities associated with chemical and biochemical footprinting methods.
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Affiliation(s)
- Pei-Sze Ng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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47
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Schnell S, Turner TE. Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 85:235-60. [PMID: 15142746 DOI: 10.1016/j.pbiomolbio.2004.01.012] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We review recent evidence illustrating the fundamental difference between cytoplasmic and test tube biochemical kinetics and thermodynamics, and showing the breakdown of the law of mass action and power-law approximation in in vivo conditions. Simulations of biochemical reactions in non-homogeneous media show that as a result of anomalous diffusion and mixing of the biochemical species, reactions follow a fractal-like kinetics. Consequently, the conventional equations for biochemical pathways fail to describe the reactions in in vivo conditions. We present a modification to fractal-like kinetics following the Zipf-Mandelbrot distribution which will enable the modelling and analysis of biochemical reactions occurring in crowded intracellular environments.
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Affiliation(s)
- S Schnell
- Centre for Mathematical Biology, Mathematical Institute, Oxford, UK.
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48
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Georlette D, Blaise V, Bouillenne F, Damien B, Thorbjarnardóttir SH, Depiereux E, Gerday C, Uversky VN, Feller G. Adenylation-dependent conformation and unfolding pathways of the NAD+-dependent DNA ligase from the thermophile Thermus scotoductus. Biophys J 2004; 86:1089-104. [PMID: 14747344 PMCID: PMC1303902 DOI: 10.1016/s0006-3495(04)74184-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Accepted: 09/22/2003] [Indexed: 10/21/2022] Open
Abstract
In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD(+)-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD(+)-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor binding induces conformational rearrangement within the active site and promotes a compaction of the enzyme. These data support an induced "open-closure" process upon adenylation, leading to the formation of the catalytically active enzyme that is able to bind DNA. These conformational changes are likely to be associated with the protein function, preventing the formation of nonproductive complexes between deadenylated ligases and DNA. In addition, enzyme adenylation significantly increases resistance of the protein to thermal denaturation and GdmCl-induced unfolding, establishing a thermodynamic link between ligand binding and increased conformational stability. Finally, chemical unfolding of deadenylated and adenylated enzyme is accompanied by accumulation of at least two equilibrium intermediates, the molten globule and premolten globule states. Maximal populations of these intermediates are shifted toward higher GdmCl concentrations in the case of the adenylated ligase. These data provide further insights into the properties of partially folded intermediates.
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Affiliation(s)
- Daphné Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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49
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Georlette D, Blaise V, Dohmen C, Bouillenne F, Damien B, Depiereux E, Gerday C, Uversky VN, Feller G. Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus. J Biol Chem 2003; 278:49945-53. [PMID: 14523019 DOI: 10.1074/jbc.m307761200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligases are important enzymes required for cellular processes such as DNA replication, recombination, and repair. NAD(+)-dependent DNA ligases are essentially restricted to eubacteria, thus constituting an attractive target in the development of novel antibiotics. Although such a project might involve the systematic testing of a vast number of chemical compounds, it can essentially gain from the preliminary deciphering of the conformational stability and structural perturbations associated with the formation of the catalytically active adenylated enzyme. We have, therefore, investigated the adenylation-induced conformational changes in the mesophilic Escherichia coli and thermophilic Thermus scotoductus NAD(+)-DNA ligases, and the resistance of these enzymes to thermal and chemical (guanidine hydrochloride) denaturation. Our results clearly demonstrate that anchoring of the cofactor induces a conformational rearrangement within the active site of both mesophilic and thermophilic enzymes accompanied by their partial compaction. Furthermore, the adenylation of enzymes increases their resistance to thermal and chemical denaturation, establishing a thermodynamic link between cofactor binding and conformational stability enhancement. Finally, guanidine hydrochloride-induced unfolding of NAD(+)-dependent DNA ligases is shown to be a complex process that involves accumulation of at least two equilibrium intermediates, the molten globule and its precursor.
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Affiliation(s)
- Daphné Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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50
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Al-Habori M. Macromolecular crowding and its role as intracellular signalling of cell volume regulation. Int J Biochem Cell Biol 2001; 33:844-64. [PMID: 11461828 DOI: 10.1016/s1357-2725(01)00058-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macromolecular crowding has been proposed as a mechanism by means of which a cell can sense relatively small changes in volume or, more accurately, the concentration of intracellular solutes. According to the macromolecular theory, the kinetics and equilibria of enzymes can be greatly influenced by small changes in the concentration of ambient, inert macromolecules. A 10% change in the concentration of intracellular proteins can lead to changes of up to a factor of ten in the thermodynamic activity of putative molecular regulatory species, and consequently, the extent to which such regulator(s) may bind to and activate membrane-associated ion transporters. The aim of this review is to examine the concept of macromolecular crowding and how it profoundly affects macromolecular association in an intact cell with particular emphasis on its implication as a sensor and a mechanism through which cell volume is regulated.
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Affiliation(s)
- M Al-Habori
- Department of Clinical Biochemistry, Faculty of Medicine and Health Sciences, University of Sana'a, PO Box 19065, Sana'a, Republic of Yemen.
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