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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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2
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Cristofalo M, Marrano CA, Salerno D, Corti R, Cassina V, Mammola A, Gherardi M, Sclavi B, Cosentino Lagomarsino M, Mantegazza F. Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers. Biochim Biophys Acta Gen Subj 2020; 1864:129725. [PMID: 32891648 DOI: 10.1016/j.bbagen.2020.129725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment. METHODS We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding. RESULTS In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively. CONCLUSIONS We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG. GENERAL SIGNIFICANCE Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.
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Affiliation(s)
- M Cristofalo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - C A Marrano
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - D Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - R Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - V Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - A Mammola
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - M Gherardi
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - B Sclavi
- Université Pierre et Marie Curie, Institut de Biologie Paris Seine, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - M Cosentino Lagomarsino
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - F Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy.
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Polotsky AA, Birshtein TM, Mercurieva AA, Leermakers FAM, Borisov OV. Unfolding of a comb-like polymer in a poor solvent: translation of macromolecular architecture in the force-deformation spectra. SOFT MATTER 2017; 13:9147-9161. [PMID: 29177317 DOI: 10.1039/c7sm01589e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A numerical self-consistent field modeling approach was employed to study the mechanical unfolding of a globule made by comb-like polymers in a poor solvent with the aim of unraveling how the macromolecular architecture affects the shape of the single-molecule force-deformation curves. We demonstrate that the dependence of the restoring force on the imposed extension of the main chain of the comb-like polymer exhibits a characteristic oscillatory shape in the intermediate deformation range. Theoretical arguments are developed that enable us to relate the shape of the patterns on the force-deformation curves to the molecular architecture (grafting density and length of the side chains) and interaction parameters. Thus, the results of our study suggest a new approach for the determination of macromolecular topology from single-molecule mechanical unfolding experiments.
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Affiliation(s)
- Alexey A Polotsky
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr, 199004 Saint Petersburg, Russia.
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Al-Obaidi H, Lawrence MJ, Buckton G. Atypical effects of incorporated surfactants on stability and dissolution properties of amorphous polymeric dispersions. ACTA ACUST UNITED AC 2016; 68:1373-1383. [PMID: 27696396 DOI: 10.1111/jphp.12645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/24/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To understand the impact of ionic and non-ionic surfactants on the dissolution and stability properties of amorphous polymeric dispersions using griseofulvin (GF) as a model for poorly soluble drugs. METHODS Solid dispersions of the poorly water-soluble drug, griseofulvin (GF) and the polymers, poly(vinylpyrrolidone) (PVP) and poly(2-hydroxypropyl methacrylate) (PHPMA), have been prepared by spray drying and bead milling and the effect of the ionic and non-ionic surfactants, namely sodium dodecyl sulphate (SDS) and Tween-80, on the physico-chemical properties of the solid dispersions studied. KEY FINDINGS The X-ray powder diffraction data and hot-stage microscopy showed a fast re-crystallisation of GF. While dynamic vapour sorption (DVS) measurements indicated an increased water uptake, slow dissolution rates were observed for the solid dispersions incorporating surfactants. The order by which surfactants free dispersions were prepared seemed critical as indicated by DVS and thermal analysis. Dispersions prepared by milling with SDS showed significantly better stability than spray-dried dispersions (drug remained amorphous for more than 6 months) as well as improved dissolution profile. CONCLUSIONS We suggest that surfactants can hinder the dissolution by promoting aggregation of polymeric chains, however that effect depends mainly on how the particles were prepared.
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Affiliation(s)
| | - M Jayne Lawrence
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Graham Buckton
- The School of Pharmacy, University College London, London, UK
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5
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Bell S, Terentjev EM. Unfolding of globular polymers by external force. J Chem Phys 2015; 143:184902. [DOI: 10.1063/1.4935393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Samuel Bell
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Eugene M. Terentjev
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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Al-Obaidi H, Lawrence MJ, Shah S, Moghul H, Al-Saden N, Bari F. Effect of drug–polymer interactions on the aqueous solubility of milled solid dispersions. Int J Pharm 2013; 446:100-5. [DOI: 10.1016/j.ijpharm.2013.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 10/27/2022]
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Polotsky AA, Smolyakova EE, Birshtein TM. Theory of Mechanical Unfolding of Homopolymer Globule: All-or-None Transition in Force-Clamp Mode vs Phase Coexistence in Position-Clamp Mode. Macromolecules 2011. [DOI: 10.1021/ma201427y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexey A. Polotsky
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, 31 Bolshoy pr., 199004 Saint-Petersburg, Russia
| | - Elizaveta E. Smolyakova
- Physical Faculty, Saint-Petersburg State University, 1 Ulyanovskaya ul., 198504 Petrodvorets, Saint-Petersburg, Russia
| | - Tatiana M. Birshtein
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, 31 Bolshoy pr., 199004 Saint-Petersburg, Russia
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8
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Polotsky AA, Daoud M, Borisov OV, Birshtein TM. A Quantitative Theory of Mechanical Unfolding of a Homopolymer Globule. Macromolecules 2009. [DOI: 10.1021/ma902302p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexey A. Polotsky
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St. Petersburg, Russia
| | - Mohamed Daoud
- Service de Physique de l’Etat Condensé CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Oleg V. Borisov
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St. Petersburg, Russia
- Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux, UMR 5254 CNRS/UPPA, Pau, France
| | - Tatiana M. Birshtein
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St. Petersburg, Russia
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9
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Polotsky AA, Charlaganov MI, Leermakers FAM, Daoud M, Borisov OV, Birshtein TM. Mechanical Unfolding of a Homopolymer Globule Studied by Self-Consistent Field Modeling. Macromolecules 2009. [DOI: 10.1021/ma9004742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexey A. Polotsky
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St.-Petersburg, Russia
| | - Marat I. Charlaganov
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, The Netherlands
| | - Frans A. M. Leermakers
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, The Netherlands
| | - Mohamed Daoud
- Service de Physique de l’Etat Condensé CEA Saclay, 91191 Gif-sur-Yvette Cedex, France, and
| | - Oleg V. Borisov
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St.-Petersburg, Russia
- Institut Pluridisciplinaire de Recherche sur l’Environnement et les Matériaux, UMR 5254 CNRS/UPPA, Pau, France
| | - Tatiana M. Birshtein
- Institute of Macromolecular Compounds, Russian Academy of Sciences 31 Bolshoy pr., 199004 St.-Petersburg, Russia
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Single homopolypeptide chains collapse into mechanically rigid conformations. Proc Natl Acad Sci U S A 2009; 106:12605-10. [PMID: 19549822 DOI: 10.1073/pnas.0900678106] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease is linked to the insertion of glutamine (Q) in the protein huntingtin, resulting in polyglutamine (polyQ) expansions that self-associate to form aggregates. While polyQ aggregation has been the subject of intense study, a correspondingly thorough understanding of individual polyQ chains is lacking. Here we demonstrate a single molecule force-clamp technique that directly probes the mechanical properties of single polyQ chains. We have made polyQ constructs of varying lengths that span the length range of normal and diseased polyQ expansions. Each polyQ construct is flanked by the I27 titin module, providing a clear mechanical fingerprint of the molecule being pulled. Remarkably, under the application of force, no extension is observed for any of the polyQ constructs. This is in direct contrast with the random coil protein PEVK of titin, which readily extends under force. Our measurements suggest that polyQ chains form mechanically stable collapsed structures. We test this hypothesis by disrupting polyQ chains with insertions of proline residues and find that their mechanical extensibility is sensitive to the position of the proline interruption. These experiments demonstrate that polyQ chains collapse to form a heterogeneous ensemble of conformations that are mechanically resilient. We further use a heat-annealing molecular dynamics protocol to extensively search the conformation space and find that polyQ can exist in highly mechanically stable compact globular conformations. The mechanical rigidity of these collapsed structures may exceed the functional ability of eukaryotic proteasomes, resulting in the accumulation of undigested polyQ sequences in vivo.
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Hemoglobin senses body temperature. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:589-600. [PMID: 19238378 DOI: 10.1007/s00249-009-0410-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 01/20/2009] [Accepted: 01/29/2009] [Indexed: 10/21/2022]
Abstract
UNLABELLED When aspirating human red blood cells (RBCs) into 1.3 mum pipettes (DeltaP = -2.3 kPa), a transition from blocking the pipette below a critical temperature T(c) = 36.3 +/- 0.3 degrees C to passing it above the T(c) occurred (micropipette passage transition). With a 1.1 mum pipette no passage was seen which enabled RBC volume measurements also above T(c). With increasing temperature RBCs lost volume significantly faster below than above a T(c) = 36.4 +/- 0.7 (volume transition). Colloid osmotic pressure (COP) measurements of RBCs in autologous plasma (25 degrees C < or = T < or = 39.5 degrees C) showed a T (c) at 37.1 +/- 0.2 degrees C above which the COP rapidly decreased (COP transition). In NMR T(1)-relaxation time measurements, the T(1) of RBCs in autologous plasma changed from a linear (r = 0.99) increment below T(c) = 37 +/- 1 degrees C at a rate of 0.023 s/K into zero slope above T(c) (RBC T(1) transition). IN CONCLUSION An amorphous hemoglobin-water gel formed in the spherical trail, the residual partial sphere of the aspirated RBC. At T(c), a sudden fluidization of the gel occurs. All changes mentioned above happen at a distinct T(c) close to body temperature. The T(c) is moved +0.8 degrees C to higher temperatures when a D(2)O buffer is used. We suggest a mechanism similar to a "glass transition" or a "colloidal phase transition". At T(c), the stabilizing Hb bound water molecules reach a threshold number enabling a partial Hb unfolding. Thus, Hb senses body temperature which must be inscribed in the primary structure of hemoglobin and possibly other proteins.
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Root DD, Yadavalli VK, Forbes JG, Wang K. Coiled-coil nanomechanics and uncoiling and unfolding of the superhelix and alpha-helices of myosin. Biophys J 2006; 90:2852-66. [PMID: 16439474 PMCID: PMC1414572 DOI: 10.1529/biophysj.105.071597] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nanomechanical properties of the coiled-coils of myosin are fundamentally important in understanding muscle assembly and contraction. Force spectra of single molecules of double-headed myosin, single-headed myosin, and coiled-coil tail fragments were acquired with an atomic force microscope and displayed characteristic triphasic force-distance responses to stretch: a rise phase (R) and a plateau phase (P) and an exponential phase (E). The R and P phases arise mainly from the stretching of the coiled-coils, with the hinge region being the main contributor to the rise phase at low force. Only the E phase was analyzable by the worm-like chain model of polymer elasticity. Restrained molecular mechanics simulations on an existing x-ray structure of scallop S2 yielded force spectra with either two or three phases, depending on the mode of stretch. It revealed that coiled-coil chains separate completely near the end of the P phase and the stretching of the unfolded chains gives rise to the E phase. Extensive conformational searching yielded a P phase force near 40 pN that agreed well with the experimental value. We suggest that the flexible and elastic S2 region, particularly the hinge region, may undergo force-induced unfolding and extend reversibly during actomyosin powerstroke.
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Affiliation(s)
- Douglas D Root
- Department of Biological Sciences, University of North Texas, Denton, 76203-5220, USA
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Craig A, Terentjev EM. Stretching globular polymers. II. Macroscopic cross-linked networks. J Chem Phys 2005; 122:194902. [PMID: 16161612 DOI: 10.1063/1.1898214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We expand upon the results for the force-extension behavior of single-collapsed polymer chains to consider the mechanical response of networks of cross-linked globular polymers in poor solvent. Force-strain curves are obtained under the affine deformation approximation for networked globules with both disordered and ordered globule conformations. Due to their large stored lengths, these networks would be capable of reaching extremely large strains. They also show anomalous nonmonotonic force-strain response, as a consequence of the nonmonotonic force-extension curves of their constituent globules. Finally, we consider the stability of ordered and disordered globules in these networks and propose means taken from biological and colloid science to stabilize networked globules.
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Affiliation(s)
- A Craig
- Cavendish Laboratory, Madingley Road, Cambridge CB3 OHE, United Kingdom
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