1
|
Garg H, Rajesh R, Vemparala S. The conformational phase diagram of neutral polymers in the presence of attractive crowders. J Chem Phys 2023; 158:114903. [PMID: 36948827 DOI: 10.1063/5.0140721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Extensive coarse-grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowder densities, the polymer predominantly shows three phases as a function of both intra-polymer and polymer-crowder interactions: (1) weak intra-polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E), (2) strong intra-polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI), and (3) strong polymer-crowder attractive interactions, regardless of intra-polymer interactions, induce a second collapsed or globular conformation that encloses bridging crowders (phase CB). The detailed phase diagram is obtained by determining the phase boundaries delineating the different phases based on an analysis of the radius of gyration as well as bridging crowders. The dependence of the phase diagram on strength of crowder-crowder attractive interactions and crowder density is clarified. We also show that when the crowder density is increased, a third collapsed phase of the polymer emerges for weak intra-polymer attractive interactions. This crowder density-induced compaction is shown to be enhanced by stronger crowder-crowder attraction and is different from the depletion-induced collapse mechanism, which is primarily driven by repulsive interactions. We also provide a unified explanation of the observed re-entrant swollen/extended conformations of the earlier simulations of weak and strongly self-interacting polymers in terms of crowder-crowder attractive interactions.
Collapse
Affiliation(s)
- Hitesh Garg
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - R Rajesh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| |
Collapse
|
2
|
Paul S, Majumder S, Das SK, Janke W. Effects of alignment activity on the collapse kinetics of a flexible polymer. SOFT MATTER 2022; 18:1978-1990. [PMID: 35023525 DOI: 10.1039/d1sm01055g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment rule adapted from the Vicsek model. Following quenching from the high-temperature coil phase to a low-temperature state point, we study the coarsening kinetics via molecular dynamics (MD) simulations using the Langevin thermostat. For the passive polymer case the low-temperature equilibrium state is a compact globule. The results from our MD simulations reveal that though the globular state is also the typical final state in the active case, the nonequilibrium pathways to arrive at such a state differ from the picture for the passive case due to the alignment interaction among the beads. We notice that deviations from the intermediate "pearl-necklace"-like arrangement, which is observed in the passive case, and the formation of more elongated dumbbell-like structures increase with increasing activity. Furthermore, it appears that while a small active force on the beads certainly makes the coarsening process much faster, there exists a nonmonotonic dependence of the collapse time on the strength of active interaction. We quantify these observations by comparing the scaling laws for the collapse time and growth of pearls with the passive case.
Collapse
Affiliation(s)
- Subhajit Paul
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Subir K Das
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore-560064, India.
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| |
Collapse
|
3
|
Dobhal A, Srivastav A, Dandekar P, Jain R. Influence of lactide vs glycolide composition of poly (lactic-co-glycolic acid) polymers on encapsulation of hydrophobic molecules: molecular dynamics and formulation studies. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2021; 32:126. [PMID: 34591178 PMCID: PMC8484083 DOI: 10.1007/s10856-021-06580-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The work demonstrates the preparation of PLGA (PLGA 50:50, PLGA 75:25) nanoparticles, to encapsulate a hydrophobic molecule (coumarin-6), using the microreactor-based continuous process. The formulations were characterized using dynamic light scattering and transmission electron microscopy to determine their size, homogeneity, zeta potential, and surface morphology. The resulting nanoparticles were safe to the CHO cells (≈80% cell survival), at the concentration of ≤600 µg/mL and were successfully taken up by the cells, as demonstrated using confocal microscopy. Moreover, imaging flow cytometry confirmed that the nanoparticles were internalized in 73.96% of the cells. Furthermore, molecular dynamics simulation and docking studies were carried out to explore the effect of polymer chain length of PLGA and lactide vs glycolide (LA:GA) ratio on their compatibility with the coumarin-6 molecules and to study the coiling and flexibility of PLGA in the presence of coumarin-6 molecules. Flory-Huggins interaction parameter (χ) was calculated for polymer chains of varying lengths and LA:GA ratio, with respect to coumarin-6. χ parameter increased with increase in polymer chain length, which indicated superior interaction of coumarin-6 with the smaller chains. Amongst all the polymeric systems, PLGA55 exhibited the strongest interaction with coumarin-6, for all the chain lengths, possibly because of their homogeneous spatial arrangements and superior binding energy. PLGA27 showed better compatibility compared to PLGA72 and PGA, whereas PLA-based polymers exhibited the least compatibility. Analysis of the radius of gyration of the polymer chains in the polymer-coumarin-6 complexes, at the end of molecular dynamics run, exhibited that the polymer chains displayed varying coiling behavior and flexibility, depending upon the relative concentrations of the polymer and coumarin-6. Factors like intra-chain interactions, spatial arrangement, inter-chain binding energies, and polymer-coumarin-6 compatibility also influenced the coiling and flexibility of polymer chains.
Collapse
Affiliation(s)
- Anurag Dobhal
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Ashu Srivastav
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| |
Collapse
|
4
|
Lerch A, Käfer F, Prévost S, Agarwal S, Karg M. Structural Insights into Polymethacrylamide-Based LCST Polymers in Solution: A Small-Angle Neutron Scattering Study. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arne Lerch
- Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Florian Käfer
- Macromolekulare Chemie II, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany
| | - Sylvain Prévost
- Institut Laue-Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Seema Agarwal
- Macromolekulare Chemie II, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany
| | - Matthias Karg
- Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| |
Collapse
|
5
|
Garaizar A, Sanchez-Burgos I, Collepardo-Guevara R, Espinosa JR. Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid-Liquid Phase Separation. Molecules 2020; 25:E4705. [PMID: 33076213 PMCID: PMC7587599 DOI: 10.3390/molecules25204705] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid-liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid-liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein-protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein-protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid-liquid phase behaviour.
Collapse
Affiliation(s)
- Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; (A.G.); (I.S.-B.); (R.C.-G.)
| | - Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; (A.G.); (I.S.-B.); (R.C.-G.)
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; (A.G.); (I.S.-B.); (R.C.-G.)
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EJ, UK
| | - Jorge R. Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; (A.G.); (I.S.-B.); (R.C.-G.)
| |
Collapse
|
6
|
Lavino AD, Carbone P, Marchisio D. MARTINI
coarse‐grained model for poly‐ε‐caprolactone in acetone‐water mixtures. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alessio D. Lavino
- Department of Applied Science and TechnologyPolitecnico di Torino Torino Italy
| | - Paola Carbone
- School of Chemical Engineering & Analytical ScienceThe University of Manchester Manchester UK
| | - Daniele Marchisio
- Department of Applied Science and TechnologyPolitecnico di Torino Torino Italy
| |
Collapse
|
7
|
Pica A, Graziano G. Why does urea have a different effect on the collapse temperature of PDEAM and PNIPAM? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
8
|
Le Fer G, Wirotius AL, Brûlet A, Garanger E, Lecommandoux S. Self-Assembly of Stimuli-Responsive Biohybrid Synthetic-b-Recombinant Block Copolypeptides. Biomacromolecules 2018; 20:254-272. [DOI: 10.1021/acs.biomac.8b01390] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Gaëlle Le Fer
- Université de Bordeaux, Bordeaux INP, ENSCBP, 16 avenue Pey-Berland, 33607 Pessac Cedex, France
- CNRS, Laboratoire de Chimie des Polymères Organiques (UMR5629), Pessac, France
| | - Anne-Laure Wirotius
- Université de Bordeaux, Bordeaux INP, ENSCBP, 16 avenue Pey-Berland, 33607 Pessac Cedex, France
- CNRS, Laboratoire de Chimie des Polymères Organiques (UMR5629), Pessac, France
| | - Annie Brûlet
- Laboratoire Léon Brillouin, UMR 12 CEA−CNRS, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Elisabeth Garanger
- Université de Bordeaux, Bordeaux INP, ENSCBP, 16 avenue Pey-Berland, 33607 Pessac Cedex, France
- CNRS, Laboratoire de Chimie des Polymères Organiques (UMR5629), Pessac, France
| | - Sébastien Lecommandoux
- Université de Bordeaux, Bordeaux INP, ENSCBP, 16 avenue Pey-Berland, 33607 Pessac Cedex, France
- CNRS, Laboratoire de Chimie des Polymères Organiques (UMR5629), Pessac, France
| |
Collapse
|
9
|
Maity H, Reddy G. Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble. J Mol Biol 2018; 430:465-478. [DOI: 10.1016/j.jmb.2017.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/28/2017] [Accepted: 09/09/2017] [Indexed: 01/21/2023]
|
10
|
Sheridan RJ, Orski SV, Jones RL, Satija SK, Beers KL. Surface interaction parameter measurement of solvated polymers via model end-tethered chains. Macromolecules 2017; 50:6668-6678. [PMID: 28970637 DOI: 10.1021/acs.macromol.7b00639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a method for the direct measurement of the relative energy of interaction between a solvated polymer and a solid interface. By tethering linear chains covalently to the surface, we ensured the idealized and constant configuration of polymer molecules for measurement, modeling, and parameter estimation. For the case of amine-terminated polystyrene bound to a glycidoxypropyl silane film submerged in cyclohexane-d12, we estimated the χ parameter for the temperature range 10.7 °C to 52.0 °C, and found a downward sloping trend that crosses the χ = 0.5 threshold at 37 °C to 40 °C, in agreement with solution estimates for the same system. We simultaneously estimated the surface interaction parameter χs at each temperature, finding a decreasing affinity of the chains for the surface with increasing temperature, consistent with empirical observations. The theoretical model shows some limitations in a stronger solvent (toluene-d8) that prevent rigorous parameter estimation, but we demonstrate a qualitative change in χ and χs towards stronger solvency and weaker surface interaction with increasing temperature.
Collapse
Affiliation(s)
- Richard J Sheridan
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Sara V Orski
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Ronald L Jones
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Sushil K Satija
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD
| | - Kathryn L Beers
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| |
Collapse
|
11
|
Dey A, Reddy G. Toroidal Condensates by Semiflexible Polymer Chains: Insights into Nucleation, Growth and Packing Defects. J Phys Chem B 2017; 121:9291-9301. [PMID: 28892379 DOI: 10.1021/acs.jpcb.7b07600] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deciphering the principles of DNA condensation is important to understand problems such as genome packing and DNA compaction for delivery in gene therapy. DNA molecules condense into toroids and spindles upon the addition of multivalent ions. Nucleation of a loop in the semiflexible DNA chain is critical for both the toroid and spindle formation. To understand the structural differences in the nucleated loop, which cause bifurcation in the condensation pathways leading to toroid or spindle formation, we performed molecular dynamics simulations using a coarse-grained bead-spring polymer model. We find that the formation of a toroid or a spindle is correlated with the orientation of the chain segments close to the loop closure in the nucleated loop. Simulations show that toroids grow in size when spindles in solution interact with a pre-existing toroid and merge into it by spooling around the circumference of the toroid, forming multimolecular toroidal condensates. The merging of spindles with toroids is facile, indicating that this should be the dominant pathway through which the toroids grow in size. The Steinhardt bond order parameter analysis of the toroid cross section shows that the chains pack in a hexagonal fashion. In agreement with the experiments there are regions in the toroid with good hexagonal packing and also with considerable disorder. The disorder in packing is due to the defects, which are propagated during the growth of toroids. In addition to the well-known crossover defect, we have identified three other forms of defects, which perturb hexagonal packing. The new defects identified in the simulations are amenable to experimental verification.
Collapse
Affiliation(s)
- Atreya Dey
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bengaluru, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bengaluru, Karnataka 560012, India
| |
Collapse
|
12
|
Guettari M, Belaidi A, Abel S, Tajouri T. Polyvinylpyrrolidone Behavior in Water/Ethanol Mixed Solvents: Comparison of Modeling Predictions with Experimental Results. J SOLUTION CHEM 2017. [DOI: 10.1007/s10953-017-0649-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
13
|
English LR, Tilton EC, Ricard BJ, Whitten ST. Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins. Proteins 2017; 85:296-311. [PMID: 27936491 DOI: 10.1002/prot.25222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Abstract
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions. To investigate sequence-modulation of IDP Rh , disordered ensembles generated by a hard sphere collision model modified with a structure-based parameterization of the solution energetics were used to parse the contributions of net charge, main chain dihedral angle bias, and excluded volume on hydrodynamic size. Ensembles for polypeptides 10-35 residues in length were then used to establish power-law scaling relationships for comparison to experimental Rh from 26 IDPs. Results showed the expected outcomes of increased hydrodynamic size from increases in excluded volume and net charge, and compaction from chain-solvent interactions. Chain bias representing intrinsic preferences for α helix and polyproline II (PPII ), however, modulated Rh with intricate dependence on the simulated propensities. PPII propensities at levels expected in IDPs correlated with heightened Rh sensitivity to even weak α helix propensities, indicating bias for common (φ, ψ) are important determinants of hydrodynamic size. Moreover, data show that IDP Rh can be predicted from sequence with good accuracy from a small set of physicochemical properties, namely intrinsic conformational propensities and net charge. Proteins 2017; 85:296-311. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Erin C Tilton
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Benjamin J Ricard
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| |
Collapse
|
14
|
Hofmann H. Understanding disordered and unfolded proteins using single-molecule FRET and polymer theory. Methods Appl Fluoresc 2016; 4:042003. [DOI: 10.1088/2050-6120/4/4/042003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
15
|
Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc 2016; 138:11714-26. [PMID: 27583570 PMCID: PMC5597961 DOI: 10.1021/jacs.6b05917] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.
Collapse
Affiliation(s)
- Alessandro Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madeleine B. Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anja Schüler
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Klaus Gast
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
16
|
Schuler B, Soranno A, Hofmann H, Nettels D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 2016; 45:207-31. [PMID: 27145874 DOI: 10.1146/annurev-biophys-062215-010915] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
Collapse
Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| |
Collapse
|
17
|
Wang J, Wu C. Reexamination of the Origin of Slow Relaxation in Semidilute Polymer Solutions—Reptation Related or Not? Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianqi Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- Heifei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Anhui, China
| | - Chi Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- Heifei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Anhui, China
| |
Collapse
|
18
|
Origin and prediction of free-solution interaction studies performed label-free. Proc Natl Acad Sci U S A 2016; 113:E1595-604. [PMID: 26960999 DOI: 10.1073/pnas.1515706113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interaction/reaction assays have led to significant scientific discoveries in the biochemical, medical, and chemical disciplines. Several fundamental driving forces form the basis of intermolecular and intramolecular interactions in chemical and biochemical systems (London dispersion, hydrogen bonding, hydrophobic, and electrostatic), and in the past three decades the sophistication and power of techniques to interrogate these processes has developed at an unprecedented rate. In particular, label-free methods have flourished, such as NMR, mass spectrometry (MS), surface plasmon resonance (SPR), biolayer interferometry (BLI), and backscattering interferometry (BSI), which can facilitate assays without altering the participating components. The shortcoming of most refractive index (RI)-based label-free methods such as BLI and SPR is the requirement to tether one of the interaction entities to a sensor surface. This is not the case for BSI. Here, our hypothesis is that the signal origin for free-solution, label-free determinations can be attributed to conformation and hydration-induced changes in the solution RI. We propose a model for the free-solution response function (FreeSRF) and show that, when quality bound and unbound structural data are available, FreeSRF correlates well with the experiment (R(2)> 0.99, Spearman rank correlation coefficients >0.9) and the model is predictive within ∼15% of the experimental binding signal. It is also demonstrated that a simple mass-weighted dη/dC response function is the incorrect equation to determine that the change in RI is produced by binding or folding event in free solution.
Collapse
|
19
|
Odagiri K, Seki K. Coil–globule transition of a polymer involved in excluded-volume interactions with macromolecules. J Chem Phys 2015; 143:134903. [DOI: 10.1063/1.4932344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kenta Odagiri
- School of Network and Information, Senshu University, Kawasaki 214-8580, Japan
| | - Kazuhiko Seki
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Tsukuba, Ibaraki 305-8565, Japan
| |
Collapse
|
20
|
Iwaki T, Ishido T, Hirano K, Lazutin AA, Vasilevskaya VV, Kenmotsu T, Yoshikawa K. Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms. J Chem Phys 2015; 142:145101. [PMID: 25877594 DOI: 10.1063/1.4916309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We performed monomolecular observations on linear and circular giant DNAs (208 kbp) in an aqueous solution by the use of fluorescence microscopy. The results showed that the degree of conformational fluctuation in circular DNA was ca. 40% less than that in linear DNA, although the long-axis length of circular DNA was only 10% smaller than that of linear DNA. Additionally, the relaxation time of a circular chain was shorter than that of a linear chain by at least one order of magnitude. The essential features of this marked difference between linear and circular DNAs were reproduced by numerical simulations on a ribbon-like macromolecule as a coarse-grained model of a long semiflexible, double-helical DNA molecule. In addition, we calculated the radius of gyration of an interacting chain in a circular form on the basis of the mean field model, which provides a better understanding of the present experimental trend than a traditional theoretical equation.
Collapse
Affiliation(s)
- Takafumi Iwaki
- Faculty of Medicine, Oita University, Hasama-cho Idaigaoka 1-1, Yufu, Oita 879-5593, Japan
| | - Tomomi Ishido
- AIST Shikoku, Hayashi-cho 2217-14, Takamatsu, Kagawa 761-0395, Japan
| | - Ken Hirano
- AIST Shikoku, Hayashi-cho 2217-14, Takamatsu, Kagawa 761-0395, Japan
| | - Alexei A Lazutin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Vavilova Street 28, V-334, GSP-1, Moscow 119991, Russia
| | - Valentina V Vasilevskaya
- A.N. Nesmeyanov Institute of Organoelement Compounds, Vavilova Street 28, V-334, GSP-1, Moscow 119991, Russia
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Science, Doshisha Universiy, Tatara Miyakodani 1-3, Kyotanabe, Kyoto 610-0321, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Science, Doshisha Universiy, Tatara Miyakodani 1-3, Kyotanabe, Kyoto 610-0321, Japan
| |
Collapse
|
21
|
Shoji T, Nohara R, Kitamura N, Tsuboi Y. A method for an approximate determination of a polymer-rich-domain concentration in phase-separated poly(N-isopropylacrylamide) aqueous solution by means of confocal Raman microspectroscopy combined with optical tweezers. Anal Chim Acta 2015; 854:118-21. [DOI: 10.1016/j.aca.2014.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/27/2014] [Accepted: 11/01/2014] [Indexed: 11/15/2022]
|
22
|
Chain collapse and aggregation in dilute solutions of poly(methyl methacrylate) below the theta temperature. Polym J 2014. [DOI: 10.1038/pj.2014.39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
23
|
Hofmann H, Nettels D, Schuler B. Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH. J Chem Phys 2014; 139:121930. [PMID: 24089742 DOI: 10.1063/1.4820490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dimensions of intrinsically disordered and unfolded proteins critically depend on the solution conditions, such as temperature, pH, ionic strength, and osmolyte or denarurant concentration. However, a quantitative understanding of how the complex combination of chain-chain and chain-solvent interactions is affected by the solvent is still missing. Here, we take a step towards this goal by investigating the combined effect of pH and denaturants on the dimensions of an unfolded protein. We use single-molecule fluorescence spectroscopy to extract the dimensions of unfolded cold shock protein (CspTm) in mixtures of the denaturants urea and guanidinium chloride (GdmCl) at neutral and acidic pH. Surprisingly, even though a change in pH from 7 to 2.9 increases the net charge of CspTm from -3.8 to +10.2, the radius of gyration of the chain is very similar under both conditions, indicating that protonation of acidic side chains at low pH results in additional hydrophobic interactions. We use a simple shared binding site model that describes the joint effect of urea and GdmCl, together with polyampholyte theory and an ion cloud model that includes the chemical free energy of counterion interactions and side chain protonation, to quantify this effect.
Collapse
Affiliation(s)
- Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | | |
Collapse
|
24
|
Wuttke R, Hofmann H, Nettels D, Borgia MB, Mittal J, Best RB, Schuler B. Temperature-dependent solvation modulates the dimensions of disordered proteins. Proc Natl Acad Sci U S A 2014; 111:5213-8. [PMID: 24706910 PMCID: PMC3986154 DOI: 10.1073/pnas.1313006111] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain-solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical "hydrophobic effect," remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse.
Collapse
Affiliation(s)
- René Wuttke
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | | | - Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, PA 18015; and
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
25
|
Tsuboi Y, Tada T, Shoji T, Kitamura N. Phase-Separation Dynamics of Aqueous Poly (N-isopropylacrylamide) Solutions: Characteristic Behavior of the Molecular Weight and Concentration Dependences. MACROMOL CHEM PHYS 2012. [DOI: 10.1002/macp.201200190] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
26
|
Chen X, Ye Y, Hao L. Atomistic picture of isothermal volume relaxation behavior of atactic polystyrene glass provided by a molecular dynamics simulation. J Chem Phys 2012; 137:044907. [PMID: 22852655 DOI: 10.1063/1.4737664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using an atomistic molecular dynamics (MD) simulation, we study the volume relaxation behavior of atactic polystyrene and attempt to correlate this macroscopic behavior with certain microscopic aspects. To this end, the gyration radius, the dimensionless relative shape anisotropy, the mean-squared displacement, and the non-Gaussian parameter are examined simultaneously. Our result shows that the structures characterized at different length scales change in a self-similar way and these changes are intimately correlated to the translational mobility of atoms. The initial incubation of structural changes at the different scales originates from the restriction of mobility due to the cage effect. The applicability of the MD simulation to the investigation of the bulk properties is discussed.
Collapse
Affiliation(s)
- Xiaoyu Chen
- School of Material Engineering, Jinling Institute of Technology, Nanjing, 211169, People's Republic of China.
| | | | | |
Collapse
|
27
|
Clough A, Chowdhury M, Jahanshahi K, Reiter G, Tsui OKC. Swelling with a Near-Θ Solvent as a Means to Modify the Properties of Polymer Thin Films. Macromolecules 2012. [DOI: 10.1021/ma301122k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew Clough
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| | - Mithun Chowdhury
- Albert-Ludwigs-Universität Physikalisches Institut, D-79104, Freiburg, Germany
| | - Kaiwan Jahanshahi
- Albert-Ludwigs-Universität Physikalisches Institut, D-79104, Freiburg, Germany
| | - Günter Reiter
- Albert-Ludwigs-Universität Physikalisches Institut, D-79104, Freiburg, Germany
- Freiburg Institute for Advanced
Studies, Albert-Ludwigs-Universität, D-79104, Freiburg, Germany
| | - Ophelia K. C. Tsui
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| |
Collapse
|
28
|
Li RN, Clough A, Yang Z, Tsui OKC. Equilibration of Polymer Films Cast from Solutions with Different Solvent Qualities. Macromolecules 2012. [DOI: 10.1021/ma202612q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ranxing Nancy Li
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| | - Andrew Clough
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| | - Zhaohui Yang
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| | - Ophelia K. C. Tsui
- Department of Physics, Boston University, Boston, Massachusetts 02215, United
States
| |
Collapse
|
29
|
Probing Properties of Polymers in Thin Films Via Dewetting. GLASS TRANSITION, DYNAMICS AND HETEROGENEITY OF POLYMER THIN FILMS 2012. [DOI: 10.1007/12_2012_174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
30
|
MAKI Y, DOBASHI T. Light Scattering of Dilute Solutions of Poly(methyl methacrylate) Below the Theta Temperature. KOBUNSHI RONBUNSHU 2012. [DOI: 10.1295/koron.69.373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
31
|
Tsuboi Y, Kikuchi K, Kitamura N, Shimomoto H, Kanaoka S, Aoshima S. Phase Separation Dynamics of Aqueous Poly [(2-ethoxy) ethoxy ethyl vinyl ether] Solutions as Explored using the Laser T-Jump Technique Combined With Photometry. MACROMOL CHEM PHYS 2011. [DOI: 10.1002/macp.201100540] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
32
|
Petridis L, Schulz R, Smith JC. Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics. J Am Chem Soc 2011; 133:20277-87. [DOI: 10.1021/ja206839u] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Roland Schulz
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| |
Collapse
|
33
|
Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2011; 22:14-20. [PMID: 22104965 DOI: 10.1016/j.sbi.2011.10.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/25/2022]
Abstract
Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.
Collapse
Affiliation(s)
- Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
34
|
England JL, Haran G. Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back. Annu Rev Phys Chem 2011; 62:257-77. [PMID: 21219136 DOI: 10.1146/annurev-physchem-032210-103531] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein stability often is studied in vitro through the use of urea and guanidinium chloride, chemical cosolvents that disrupt protein native structure. Much controversy still surrounds the underlying mechanism by which these molecules denature proteins. Here we review current thinking on various aspects of chemical denaturation. We begin by discussing classic models of protein folding and how the effects of denaturants may fit into this picture through their modulation of the collapse, or coil-globule transition, which typically precedes folding. Subsequently, we examine recent molecular dynamics simulations that have shed new light on the possible microscopic origins of the solvation effects brought on by denaturants. It seems likely that both denaturants operate by facilitating solvation of hydrophobic regions of proteins. Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition.
Collapse
Affiliation(s)
- Jeremy L England
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | | |
Collapse
|
35
|
Yoshikawa K. Kinetics of collapse and decollapse of a single double-stranded DNA chain. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/masy.19961060134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
|
37
|
Raegen A, Chowdhury M, Calers C, Schmatulla A, Steiner U, Reiter G. Aging of thin polymer films cast from a near-theta solvent. PHYSICAL REVIEW LETTERS 2010; 105:227801. [PMID: 21231423 DOI: 10.1103/physrevlett.105.227801] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Indexed: 05/30/2023]
Abstract
We have examined the aging behavior of spin-cast thin polymer films as a function of their processing history. Films prepared from solutions close to the Θ temperature were aged for varying times at room temperature, followed by a dewetting experiment above the glass transition temperature of the polymer. The characteristic aging time varied strongly with the quality of the solvent, which is attributed to distorted chain conformations in the as-cast films. This is an indication for the nonequilibrium nature of thin polymer films, possibly causing some of their unexplained properties.
Collapse
Affiliation(s)
- Adam Raegen
- Albert-Ludwigs-Universität Physikalisches Institut, 79104, Freiburg, Germany
| | | | | | | | | | | |
Collapse
|
38
|
Hu J, Wang D, Xu J, Zhu Z, Liu S. Contraction and Collapsing Kinetics of Single Synthetic Polymer Chains at Small Quench Depths. MACROMOL CHEM PHYS 2010. [DOI: 10.1002/macp.201000476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
39
|
Lages S, Michels R, Huber K. Coil-Collapse and Coil-Aggregation due to the Interaction of Cu2+ and Ca2+ Ions with Anionic Polyacylate Chains in Dilute Solution. Macromolecules 2010. [DOI: 10.1021/ma9027239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. Lages
- Department Chemie, Universität Paderborn, Fakultät für Naturwissenschaften, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - R. Michels
- Department Chemie, Universität Paderborn, Fakultät für Naturwissenschaften, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - K. Huber
- Department Chemie, Universität Paderborn, Fakultät für Naturwissenschaften, Warburger Strasse 100, D-33098 Paderborn, Germany
| |
Collapse
|
40
|
Zhang WZ, Chen XD, Yang J, Luo WA, Zhang MQ. Quantitative Description of Aggregation and Dissociation of Polystyrene Chains in Cyclohexane Solutions by Resonance Light Scattering Technique. J Phys Chem B 2010; 114:1301-6. [DOI: 10.1021/jp909925v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wen Zhi Zhang
- Key Laboratory for Polymer Composite and Functional Materials of the Ministry of Education, DSAPM Lab, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xu Dong Chen
- Key Laboratory for Polymer Composite and Functional Materials of the Ministry of Education, DSAPM Lab, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jin Yang
- Key Laboratory for Polymer Composite and Functional Materials of the Ministry of Education, DSAPM Lab, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei-ang Luo
- Key Laboratory for Polymer Composite and Functional Materials of the Ministry of Education, DSAPM Lab, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming Qiu Zhang
- Key Laboratory for Polymer Composite and Functional Materials of the Ministry of Education, DSAPM Lab, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
41
|
Aseyev V, Tenhu H, Winnik FM. Non-ionic Thermoresponsive Polymers in Water. ADVANCES IN POLYMER SCIENCE 2010. [DOI: 10.1007/12_2010_57] [Citation(s) in RCA: 374] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
42
|
Lages S, Lindner P, Sinha P, Kiriy A, Stamm M, Huber K. Formation of Ca2+-Induced Intermediate Necklace Structures of Polyacrylate Chains. Macromolecules 2009. [DOI: 10.1021/ma8027547] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Lages
- Chemsitry Department, Universität Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Peter Lindner
- Institute Laue-Langevin, LSS Group, B.P. 156, 6, rue Jules Horowitz, F-38042, Grenoble, Cedex 9, France
| | - Prashant Sinha
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Anton Kiriy
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Manfred Stamm
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Klaus Huber
- Chemsitry Department, Universität Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| |
Collapse
|
43
|
Kamata K, Araki T, Tanaka H. Hydrodynamic selection of the kinetic pathway of a polymer coil-globule transition. PHYSICAL REVIEW LETTERS 2009; 102:108303. [PMID: 19392167 DOI: 10.1103/physrevlett.102.108303] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Indexed: 05/27/2023]
Abstract
Recently, the role of hydrodynamic interactions in the selection of a kinetic pathway for phase transitions has attracted considerable attention. Here we study this problem numerically by taking as an example a coil-globule transition of a single polymer, which is a prototype model of protein folding. When a swollen polymer collapses into a globule state, hydrodynamic interactions accelerate the transition. We find, on the other hand, that when a rather compact polymer collapses into the same final state, hydrodynamic interactions decelerate the transition due to a slow squeezing process of the solvent. We reveal that the degree of the initial enhancement of anisotropy of the polymer configuration determines whether hydrodynamic interactions accelerate or decelerate the collapsing dynamics. We also discuss the possible relevance of squeezing flow effects in protein folding.
Collapse
Affiliation(s)
- Kumiko Kamata
- Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | | | | |
Collapse
|
44
|
Abstract
The coil-globule transition, a tenet of the physics of polymers, has been identified in recent years as an important unresolved aspect of the initial stages of the folding of proteins. We describe the basics of the collapse transition, starting with homopolymers and continuing with proteins. Studies of denatured-state collapse under equilibrium are then presented. An emphasis is placed on single-molecule fluorescence experiments, which are particularly useful for measuring properties of the denatured state even under conditions of coexistence with the folded state. Attempts to understand the dynamics of collapse, both theoretically and experimentally, are then described. Only an upper limit for the rate of collapse has been obtained so far. Improvements in experimental and theoretical methodology are likely to continue to push our understanding of the importance of the denatured-state thermodynamics and dynamics for protein folding in the coming years.
Collapse
Affiliation(s)
- Guy Ziv
- Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovot, Israel. E-mail:
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovot, Israel. E-mail:
| |
Collapse
|
45
|
Vitalis A, Wang X, Pappu RV. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization. J Mol Biol 2008; 384:279-97. [PMID: 18824003 PMCID: PMC2847503 DOI: 10.1016/j.jmb.2008.09.026] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 09/01/2008] [Accepted: 09/10/2008] [Indexed: 12/28/2022]
Abstract
Aggregation of expanded polyglutamine tracts is associated with nine different neurodegenerative diseases, including Huntington's disease. Experiments and computer simulations have demonstrated that monomeric forms of polyglutamine molecules sample heterogeneous sets of collapsed structures in water. The current work focuses on a mechanistic characterization of polyglutamine homodimerization as a function of chain length and temperature. These studies were carried out using molecular simulations based on a recently developed continuum solvation model that was designed for studying conformational and binding equilibria of intrinsically disordered molecules such as polyglutamine systems. The main results are as follows: Polyglutamine molecules form disordered, collapsed globules in aqueous solution. These molecules spontaneously associate at conditions approaching those of typical in vitro experiments for chains of length N>/=15. The spontaneity of these homotypic associations increases with increasing chain length and decreases with increasing temperature. Similar and generic driving forces govern both collapse and spontaneous homodimerization of polyglutamine in aqueous milieus. Collapse and dimerization maximize self-interactions and reduce the interface between polyglutamine molecules and the surrounding solvent. Other than these generic considerations, there do not appear to be any specific structural requirements for either chain collapse or chain dimerization; that is, both collapse and dimerization are nonspecific in that disordered globules form disordered dimers. In fact, it is shown that the driving force for intermolecular associations is governed by spontaneous conformational fluctuations within monomeric polyglutamine. These results suggest that polyglutamine aggregation is unlikely to follow a homogeneous nucleation mechanism with the monomer as the critical nucleus. Instead, the results support the formation of disordered, non-beta-sheet-like soluble molten oligomers as early intermediates--a proposal that is congruent with recent experimental data.
Collapse
Affiliation(s)
- Andreas Vitalis
- Department of Biomedical Engineering and Center for Computational Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130
| | | | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Computational Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, MO 63130
| |
Collapse
|
46
|
Zhou K, Lu Y, Li J, Shen L, Zhang G, Xie Z, Wu C. The Coil-to-Globule-to-Coil Transition of Linear Polymer Chains in Dilute Aqueous Solutions: Effect of Intrachain Hydrogen Bonding. Macromolecules 2008. [DOI: 10.1021/ma8019128] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kejin Zhou
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Yijie Lu
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Junfang Li
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Lei Shen
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Guangzhao Zhang
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Zuowei Xie
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Chi Wu
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| |
Collapse
|
47
|
On Mechanism of Intermediate-Sized Circular DNA Compaction Mediated by Spermine: Contribution of Fluorescence Lifetime Correlation Spectroscopy. J Fluoresc 2008; 18:679-84. [DOI: 10.1007/s10895-008-0345-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
|
48
|
Tsuboi Y, Yoshida Y, Okada K, Kitamura N. Phase Separation Dynamics of Aqueous Solutions of Thermoresponsive Polymers Studied by a Laser T-Jump Technique. J Phys Chem B 2008; 112:2562-5. [DOI: 10.1021/jp711128s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasuyuki Tsuboi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuhiro Yoshida
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kensaku Okada
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Noboru Kitamura
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| |
Collapse
|
49
|
Kaiser A, Schmidt AM. Phase Behavior of Polystyrene-Brush-Coated Nanoparticles in Cyclohexane. J Phys Chem B 2008; 112:1894-8. [DOI: 10.1021/jp076218q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas Kaiser
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Annette M. Schmidt
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| |
Collapse
|
50
|
|