1
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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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2
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Sun H, Yao C, You K, Chen C, Liu S, Xu Z. Nanopore single-molecule biosensor in protein denaturation analysis. Anal Chim Acta 2023; 1243:340830. [PMID: 36697181 DOI: 10.1016/j.aca.2023.340830] [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: 11/10/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China.
| | - Chuan Yao
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Kaibo You
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Can Chen
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Shuoshuo Liu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Zhihong Xu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
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3
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Kim S, Lee WB, de Souza NR, Choi SH. QENS study on local segmental dynamics of polyelectrolytes in complex coacervates. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Denayer M, Vekeman J, Tielens F, De Proft F. Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study. Phys Chem Chem Phys 2021; 23:25374-25387. [PMID: 34751286 DOI: 10.1039/d1cp04346c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we present the development of a novel, quantitative solubility descriptor based on the non-covalent interaction index. It is presented as a more insightful alternative to Hansen's solubility parameters and the COSMO model to assess and predict polymer solubility in different solvents. To this end, we studied the solvation behaviour as a function of the chain length of a single chain of arguably the most simple polymer, polyethylene, in anisole (solvent) and methanol (poor solvent) via molecular dynamics simulations. It was found that in anisole the solute maximized its interface with the solvent, whereas in methanol the macromolecule formed rod-like structures by folding on itself once the chain length surpassed a certain barrier. We assessed this behaviour - which can be related to solubility - quantitatively and qualitatively via well-known descriptors, namely the solvation free energy, and the solvent accessible surface area. In addition, we propose the non-covalent interaction (NCI) index as a versatile descriptor, providing information on the strength, as well as the nature, of the solute-solvent interactions, the solute's intramolecular interactions and on the solute's conformation, both qualitatively and quantitatively. Finally, as a quantitative measure for solubility, defined in this context as the solute's tendency to maximize its interactions with the solvent, we propose two new NCI-based descriptors: the relative integrated NCI density and the integrated NCI difference. The former represents the quantitative difference in solute-solvent interactions between a fully extended coil and the actual conformation during simulation and the latter the quantitative difference between the intermolecular (solute-solvent) and the intramolecular (in the solute) non-covalent interactions. The easy interpretation and calculation of these novel quantities open up the possibility of fast, reliable and insightful high-throughput screening of different (anti)solvent and solute combinations.
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Affiliation(s)
- Mats Denayer
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
| | - Jelle Vekeman
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
| | - Frederik Tielens
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
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5
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Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
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6
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Dhattarwal HS, Remsing RC, Kashyap HK. Intercalation-deintercalation of water-in-salt electrolytes in nanoscale hydrophobic confinement. NANOSCALE 2021; 13:4195-4205. [PMID: 33586725 DOI: 10.1039/d0nr08163a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intercalation-deintercalation of water-in-salt (WIS) electrolytes in nanoscale confinement is an important phenomenon relevant to energy storage and self-assembly applications. In this article, we use molecular simulations to investigate the effects of intersurface separation on the structure and free energy underlying the intercalation-deintercalation of the Li bis(trifluoromethane)sulfonimide ([Li][TFSI]) water-in-salt (WIS) electrolyte confined between nanoscale hydrophobic surfaces. We employ enhanced sampling to estimate the free energy profiles for the intercalation behaviour of WIS in confining sheets at several intersurface separations. We observe that the relative stability of the condensed and vapour phases of WIS in the confinement depends on the separation between the confining surfaces and the WIS concentration. We find that the critical separation at which the condensed and vapour phases are equally stable in confinement depends on the concentration of WIS. The relative height of the free energy barrier also strongly depends on the concentration of [Li][TFSI] inside the confined space, and we find that this concentration dependence can be attributed to changes in line tension. The process of deintercalation passes through vapour tube formation inside the confined space, and this process is initiated by vapour bubble formation. The size of the critical vapour tube required for spontaneous evaporation of WIS from the confinement is also found to depend on the intersurface separation and WIS concentration.
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Affiliation(s)
- Harender S Dhattarwal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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7
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Halder R, Jana B. Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution. Proteins 2020; 89:116-125. [PMID: 32860277 DOI: 10.1002/prot.25999] [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: 11/21/2019] [Revised: 08/07/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.
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Affiliation(s)
- Ritaban Halder
- School of Chemical Sciences, Indian Association for the cultivation of Science, Jadavpur, Kolkata, West Bengal, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the cultivation of Science, Jadavpur, Kolkata, West Bengal, India
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8
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Mirdha L, Chakraborty H. Fluorescence quenching by ionic liquid as a potent tool to study protein unfolding intermediates. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113408] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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9
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Ganguly P, Shea JE. Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation. J Phys Chem Lett 2019; 10:7406-7413. [PMID: 31721587 DOI: 10.1021/acs.jpclett.9b03004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment 1NLYIQWL7 of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
- Department of Physics , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
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10
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Parui S, Jana B. Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. J Phys Chem B 2019; 123:8889-8900. [DOI: 10.1021/acs.jpcb.9b06859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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11
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A molecular dynamics approach to nanostructuring of particles produced via aerosol cationic photopolymerization. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2018.10.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents. Phys Chem Chem Phys 2018; 20:29389-29398. [PMID: 30451257 DOI: 10.1039/c8cp04421j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia - 80126 Napoli, Italy.
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13
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Tomar DS, Ramesh N, Asthagiri D. Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides. J Chem Phys 2018; 148:222822. [DOI: 10.1063/1.5022465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Dheeraj S. Tomar
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21208, USA
| | - Niral Ramesh
- Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005-1892, USA
| | - D. Asthagiri
- Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005-1892, USA
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14
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The unusual visible fluorescence violating the Kasha's rule suggests the aggregation of guanidinium carbonate in its aqueous medium. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Balos V, Bonn M, Hunger J. Anionic and cationic Hofmeister effects are non-additive for guanidinium salts. Phys Chem Chem Phys 2017; 19:9724-9728. [PMID: 28361132 DOI: 10.1039/c7cp00790f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand specific ion effects on a molecular level we explore the effect of salts on the rotational mobility of a model amide using dielectric spectroscopy. Based on our previous studies on the effect of strong denaturing anions or cations, here we study the additivity of the anionic and cationic effect. Using salts consisting of denaturing spherical anions and spherical cations we find such salts to affect the amide according to what one expects based on the additive activity of the individual ions. The guanidinium (Gdm+) cation appears to be a notable exception, as our results suggest that GdmI (and accordingly GdmSCN) is less efficient in hindering the rotation of the amide than KI or GdmCl.
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Affiliation(s)
- V Balos
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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16
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Parimal S, Garde S, Cramer SM. Effect of guanidine and arginine on protein–ligand interactions in multimodal cation‐exchange chromatography. Biotechnol Prog 2017; 33:435-447. [DOI: 10.1002/btpr.2419] [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: 11/30/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Siddharth Parimal
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute110 8th StreetTroy NY12180
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute110 8th StreetTroy NY12180
| | - Steven M. Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute110 8th StreetTroy NY12180
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17
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Williams C, Dougherty ML, Makaroff K, Stapleton J, Konkolewicz D, Berberich JA, Page RC. Strategies for Biophysical Characterization of Protein–Polymer Conjugates. Methods Enzymol 2017; 590:93-114. [DOI: 10.1016/bs.mie.2016.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model. Biophys J 2016; 110:1510-1522. [PMID: 27074677 DOI: 10.1016/j.bpj.2016.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
Conformational states of the metastable drkN SH3 domain were characterized using single-molecule fluorescence techniques. Under nondenaturing conditions, two Förster resonance energy transfer (FRET) populations were observed that corresponded to a folded and an unfolded state. FRET-estimated radii of gyration and hydrodynamic radii estimated by fluorescence correlation spectroscopy of the two coexisting conformations are in agreement with previous ensemble x-ray scattering and NMR measurements. Surprisingly, when exposed to high concentrations of urea and GdmCl denaturants, the protein still exhibits two distinct FRET populations. The dominant conformation is expanded, showing a low FRET efficiency, consistent with the expected behavior of a random chain with excluded volume. However, approximately one-third of the drkN SH3 conformations showed high, nearly 100%, FRET efficiency, which is shown to correspond to denaturation-induced looped conformations that remain stable on a timescale of at least 100 μs. These loops may contain interconverting conformations that are more globally collapsed, hairpin-like, or circular, giving rise to the observed heterogeneous broadening of this population. Although the underlying mechanism of chain looping remains elusive, FRET experiments in formamide and dimethyl sulfoxide suggest that interactions between hydrophobic groups in the distal regions may play a significant role in the formation of the looped state.
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19
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Parui S, Manna RN, Jana B. Destabilization of Hydrophobic Core of Chicken Villin Headpiece in Guanidinium Chloride Induced Denaturation: Hint of π-Cation Interaction. J Phys Chem B 2016; 120:9599-607. [DOI: 10.1021/acs.jpcb.6b06325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700
032, India
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20
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Balos V, Bonn M, Hunger J. Quantifying transient interactions between amide groups and the guanidinium cation. Phys Chem Chem Phys 2016; 17:28539-43. [PMID: 26461077 DOI: 10.1039/c5cp04619j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the interaction of the guanidinium cation, a widely used protein denaturant, with amide groups, the common structural motif of proteins. Our results provide evidence for direct contact between guanidinium and ∼2 amide groups, but the interaction is transient and weaker than for other cations with high charge-density.
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Affiliation(s)
- V Balos
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - M Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - J Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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21
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Rotondo CM, Marrone L, Goodfellow VJ, Ghavami A, Labbé G, Spencer J, Dmitrienko GI, Siemann S. Arginine-containing peptides as potent inhibitors of VIM-2 metallo-β-lactamase. Biochim Biophys Acta Gen Subj 2015; 1850:2228-38. [DOI: 10.1016/j.bbagen.2015.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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22
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Huang K, Gast S, Ma CD, Abbott NL, Szlufarska I. Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study. J Phys Chem B 2015; 119:13152-9. [DOI: 10.1021/acs.jpcb.5b05220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Sebastian Gast
- Institute
of Chemical Engineering, University of Stuttgart, Stuttgart 70199, Germany
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23
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Bandyopadhyay D, Bhanja K, Mohan S, Ghosh SK, Choudhury N. Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study. J Phys Chem B 2015; 119:11262-74. [DOI: 10.1021/acs.jpcb.5b03064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - K. Bhanja
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy Water Division and ‡Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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24
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How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory. Proc Natl Acad Sci U S A 2015; 112:9270-5. [PMID: 26170324 DOI: 10.1073/pnas.1511780112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is currently the consensus belief that protective osmolytes such as trimethylamine N-oxide (TMAO) favor protein folding by being excluded from the vicinity of a protein, whereas denaturing osmolytes such as urea lead to protein unfolding by strongly binding to the surface. Despite there being consensus on how TMAO and urea affect proteins as a whole, very little is known as to their effects on the individual mechanisms responsible for protein structure formation, especially hydrophobic association. In the present study, we use single-molecule atomic force microscopy and molecular dynamics simulations to investigate the effects of TMAO and urea on the unfolding of the hydrophobic homopolymer polystyrene. Incorporated with interfacial energy measurements, our results show that TMAO and urea act on polystyrene as a protectant and a denaturant, respectively, while complying with Tanford-Wyman preferential binding theory. We provide a molecular explanation suggesting that TMAO molecules have a greater thermodynamic binding affinity with the collapsed conformation of polystyrene than with the extended conformation, while the reverse is true for urea molecules. Results presented here from both experiment and simulation are in line with earlier predictions on a model Lennard-Jones polymer while also demonstrating the distinction in the mechanism of osmolyte action between protein and hydrophobic polymer. This marks, to our knowledge, the first experimental observation of TMAO-induced hydrophobic collapse in a ternary aqueous system.
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25
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Ou SC, Cui D, Wezowicz M, Taufer M, Patel S. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations. J Comput Chem 2015; 36:1196-212. [PMID: 25868455 PMCID: PMC4445429 DOI: 10.1002/jcc.23906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/22/2015] [Accepted: 02/21/2015] [Indexed: 11/06/2022]
Abstract
In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces.
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Affiliation(s)
- Shu-Ching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Di Cui
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Matthew Wezowicz
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Michela Taufer
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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26
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Heiles S, Cooper RJ, DiTucci MJ, Williams ER. Hydration of guanidinium depends on its local environment. Chem Sci 2015; 6:3420-3429. [PMID: 28706704 PMCID: PMC5490459 DOI: 10.1039/c5sc00618j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/14/2015] [Indexed: 01/10/2023] Open
Abstract
Hydration of gaseous guanidinium (Gdm+) with up to 100 water molecules attached was investigated using infrared photodissociation spectroscopy in the hydrogen stretch region between 2900 and 3800 cm-1. Comparisons to IR spectra of low-energy computed structures indicate that at small cluster size, water interacts strongly with Gdm+ with three inner shell water molecules each accepting two hydrogen bonds from adjacent NH2 groups in Gdm+. Comparisons to results for tetramethylammonium (TMA+) and Na+ enable structural information for larger clusters to be obtained. The similarity in the bonded OH region for Gdm(H2O)20+vs. Gdm(H2O)100+ and the similarity in the bonded OH regions between Gdm+ and TMA+ but not Na+ for clusters with <50 water molecules indicate that Gdm+ does not significantly affect the hydrogen-bonding network of water molecules at large size. These results indicate that the hydration around Gdm+ changes for clusters with more than about eight water molecules to one in which inner shell water molecules only accept a single H-bond from Gdm+. More effective H-bonding drives this change in inner-shell water molecule binding to other water molecules. These results show that hydration of Gdm+ depends on its local environment, and that Gdm+ will interact with water even more strongly in an environment where water is partially excluded, such as the surface of a protein. This enhanced hydration in a limited solvation environment may provide new insights into the effectiveness of Gdm+ as a protein denaturant.
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Affiliation(s)
- Sven Heiles
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Richard J Cooper
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Matthew J DiTucci
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
| | - Evan R Williams
- Department of Chemistry , University of California , B42 Hildebrand Hall , Berkeley , CA 94720 , USA .
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27
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Wu E, Coppens MO, Garde S. Role of arginine in mediating protein-carbon nanotube interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1683-1692. [PMID: 25575129 DOI: 10.1021/la5043553] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arginine-rich proteins (e.g., lysozyme) or poly-L-arginine peptides have been suggested as solvating and dispersing agents for single-wall carbon nanotubes (CNTs) in water. In addition, protein structure-function in porous and hydrophobic materials is of broad interest. The amino acid residue, arginine (Arg(+)), has been implicated as an important mediator of protein/peptide-CNT interactions. To understand the structural and thermodynamic aspects of this interaction at the molecular level, we employ molecular dynamics (MD) simulations of the protein lysozyme in the interior of a CNT, as well as of free solutions of Arg(+) in the presence of a CNT. To dissect the Arg(+)-CNT interaction further, we also perform simulations of aqueous solutions of the guanidinium ion (Gdm(+)) and the norvaline (Nva) residue in the presence of a CNT. We show that the interactions of lysozyme with the CNT are mediated by the surface Arg(+) residues. The strong interaction of Arg(+) residue with the CNT is primarily driven by the favorable interactions of the Gdm(+) group with the CNT wall. The Gdm(+) group is not as well-hydrated on its flat sides, which binds to the CNT wall. This is consistent with a similar binding of Gdm(+) ions to a hydrophobic polymer. In contrast, the Nva residue, which lacks the Gdm(+) group, binds to the CNT weakly. We present details of the free energy of binding, molecular structure, and dynamics of these solutes on the CNT surface. Our results highlight the important role of Arg(+) residues in protein-CNT or protein-carbon-based material interactions. Such interactions could be manipulated precisely through protein engineering, thereby offering control over protein orientation and structure on CNTs, graphene, or other hydrophobic interfaces.
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Affiliation(s)
- Eugene Wu
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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28
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Ma CD, Wang C, Acevedo-Vélez C, Gellman SH, Abbott NL. Modulation of hydrophobic interactions by proximally immobilized ions. Nature 2015; 517:347-50. [DOI: 10.1038/nature14018] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/27/2014] [Indexed: 11/09/2022]
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29
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Cui D, Ou SC, Patel S. Protein denaturants at aqueous-hydrophobic interfaces: self-consistent correlation between induced interfacial fluctuations and denaturant stability at the interface. J Phys Chem B 2015; 119:164-78. [PMID: 25536388 PMCID: PMC4291035 DOI: 10.1021/jp507203g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/21/2014] [Indexed: 01/16/2023]
Abstract
The notion of direct interaction between denaturing cosolvent and protein residues has been proposed in dialogue relevant to molecular mechanisms of protein denaturation. Here we consider the correlation between free energetic stability and induced fluctuations of an aqueous-hydrophobic interface between a model hydrophobically associating protein, HFBII, and two common protein denaturants, guanidinium cation (Gdm(+)) and urea. We compute potentials of mean force along an order parameter that brings the solute molecule close to the known hydrophobic region of the protein. We assess potentials of mean force for different relative orientations between the protein and denaturant molecule. We find that in both cases of guanidinium cation and urea relative orientations of the denaturant molecule that are parallel to the local protein-water interface exhibit greater stability compared to edge-on or perpendicular orientations. This behavior has been observed for guanidinium/methylguanidinium cations at the liquid-vapor interface of water, and thus the present results further corroborate earlier findings. Further analysis of the induced fluctuations of the aqueous-hydrophobic interface upon approach of the denaturant molecule indicates that the parallel orientation, displaying a greater stability at the interface, also induces larger fluctuations of the interface compared to the perpendicular orientations. The correlation of interfacial stability and induced interface fluctuation is a recurring theme for interface-stable solutes at hydrophobic interfaces. Moreover, observed correlations between interface stability and induced fluctuations recapitulate connections to local hydration structure and patterns around solutes as evidenced by experiment (Cooper et al., J. Phys. Chem. A 2014, 118, 5657.) and high-level ab initio/DFT calculations (Baer et al., Faraday Discuss 2013, 160, 89).
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Affiliation(s)
- Di Cui
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shu-Ching Ou
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sandeep Patel
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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30
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Zhang L, Jiang L, Liu Y, Yin Q. Ionic strength-modulated catalytic efficiency of a multienzyme cascade nanoconfined on charged hierarchical scaffolds. RSC Adv 2015. [DOI: 10.1039/c5ra04512f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the effect of ionic strength on the efficiency of this enzyme cascade within charged hierarchical nanospace is not only fundamentally interesting, but also important for translating biochemical pathways to noncellular environments.
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Affiliation(s)
- Ling Zhang
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Li Jiang
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Yuan Liu
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Qihe Yin
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
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31
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Wu E, Garde S. Lengthscale-Dependent Solvation and Density Fluctuations in n-Octane. J Phys Chem B 2014; 119:9287-94. [DOI: 10.1021/jp509912v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eugene Wu
- Howard P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Shekhar Garde
- Howard P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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32
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Schaller A, Connors NK, Dwyer MD, Oelmeier SA, Hubbuch J, Middelberg APJ. Computational study of elements of stability of a four-helix bundle protein biosurfactant. J Comput Aided Mol Des 2014; 29:47-58. [PMID: 25323391 DOI: 10.1007/s10822-014-9803-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/10/2014] [Indexed: 10/24/2022]
Abstract
Biosurfactants are surface-active molecules produced principally by microorganisms. They are a sustainable alternative to chemically-synthesized surfactants, having the advantages of being non-toxic, highly functional, eco-friendly and biodegradable. However they are currently only used in a few industrial products due to costs associated with production and purification, which exceed those for commodity chemical surfactants. DAMP4, a member of a four-helix bundle biosurfactant protein family, can be produced in soluble form and at high yield in Escherichia coli, and can be recovered using a facile thermal phase-separation approach. As such, it encompasses an interesting synergy of biomolecular and chemical engineering with prospects for low-cost production even for industrial sectors. DAMP4 is highly functional, and due to its extraordinary thermal stability it can be purified in a simple two-step process, in which the combination of high temperature and salt leads to denaturation of all contaminants, whereas DAMP4 stays stable in solution and can be recovered by filtration. This study aimed to characterize and understand the fundamental drivers of DAMP4 stability to guide further process and surfactant design studies. The complementary use of experiments and molecular dynamics simulation revealed a broad pH and temperature tolerance for DAMP4, with a melting point of 122.4 °C, suggesting the hydrophobic core as the major contributor to thermal stability. Simulation of systematically created in silico variants of DAMP4 showed an influence of number and location of hydrophilic mutations in the hydrophobic core on stability, demonstrating a tolerance of up to three mutations before a strong loss in stability occurred. The results suggest a consideration of a balance of stability, functionality and kinetics for new designs according to their application, aiming for maximal functionality but at adequate stability to allow for cost-efficient production using thermal phase separation approaches.
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Affiliation(s)
- Andrea Schaller
- Centre for Biomolecular Engineering, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
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33
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Parimal S, Cramer SM, Garde S. Application of a Spherical Harmonics Expansion Approach for Calculating Ligand Density Distributions around Proteins. J Phys Chem B 2014; 118:13066-76. [DOI: 10.1021/jp506849k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Siddharth Parimal
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Steven M. Cramer
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Shekhar Garde
- Howard
P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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34
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Macdonald RD, Khajehpour M. Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions. Biophys Chem 2014; 196:25-32. [PMID: 25268875 DOI: 10.1016/j.bpc.2014.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022]
Abstract
Guanidinium chloride (GdmCl) is one of the most common protein denaturants. Although GdmCl is well known in the field of protein folding, the mechanism by which it denatures proteins is not well understood. In fact, there are few studies looking at its effects on hydrophobic interactions. In this work the effect of GdmCl on hydrophobic interactions has been studied by observing how the denaturant influences model systems of phenyl and alkyl hydrophobic contact pairs. Contact pair formation is monitored through the use of fluorescence spectroscopy, i.e., measuring the intrinsic phenol fluorescence being quenched by carboxylate ions. Hydrophobic interactions are isolated from other interactions through a previously developed methodology. The results show that GdmCl does not significantly affect hydrophobic interactions between small moieties such as methyl groups and phenol; while on the other hand, the interaction of larger hydrophobes such as hexyl and heptyl groups with phenol is significantly destabilized.
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Affiliation(s)
- Ryan D Macdonald
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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35
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An alternative explanation for the collapse of unfolded proteins in an aqueous mixture of urea and guanidinium chloride. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Cooper RJ, Heiles S, DiTucci MJ, Williams ER. Hydration of Guanidinium: Second Shell Formation at Small Cluster Size. J Phys Chem A 2014; 118:5657-66. [DOI: 10.1021/jp506429a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Richard J. Cooper
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Sven Heiles
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew J. DiTucci
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R. Williams
- Department
of Chemistry, University of California, Berkeley, California 94720-1460, United States
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37
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Dasgupta A, Udgaonkar JB, Das P. Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure. J Phys Chem B 2014; 118:6380-92. [DOI: 10.1021/jp410019f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amrita Dasgupta
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Payel Das
- Computational
Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan
Road, Yorktown Heights, New
York 10598, United States
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38
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Jha SK, Marqusee S. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride. Proc Natl Acad Sci U S A 2014; 111:4856-61. [PMID: 24639503 PMCID: PMC3977270 DOI: 10.1073/pnas.1315453111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).
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Affiliation(s)
| | - Susan Marqusee
- California Institute for Quantitative Biosciences and
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
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39
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Mandal M, Mukhopadhyay C. Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052708. [PMID: 24329297 DOI: 10.1103/physreve.88.052708] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/05/2013] [Indexed: 06/03/2023]
Abstract
An all-atom molecular dynamics simulation shows concentration-dependent like-charge ion pairing of the guanidinium ion in an aqueous solution of guanidinium chloride. We have observed two types of like-charge ion pairing for guanidinium ions, namely, stacked ion pairs and solvent-separated ion pairs. Interestingly, both of these like-charge ion-pair formations are dependent on the concentration of guanidinium chloride in water. The probability of stacked like-charge ion-pair formation decreases, whereas, the probability of solvent-separated like-charge pairing increases as the concentration of guanidinium chloride increases, which is shown from radial distribution functions and is confirmed from the energy calculations. Besides like-charge ion-pair formation, we also investigated guanidinium chloride induced changes in water structure. Hydrogen-bond analysis indicates that guanidinium chloride does not alter the strict-hydrogen-bonding patterns of water, whereas, it breaks the bend-hydrogen bond and the non-hydrogen-bonding patterns. Tetrahedral order, nearest neighbor orientation, and distance distribution of water molecules around a probe water molecule show the extent of water structure distortion.
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Affiliation(s)
- Manoj Mandal
- Department of Chemistry, University of Calcutta 92, A.P.C. Road, Kolkata-700 009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta 92, A.P.C. Road, Kolkata-700 009, India
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40
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Koishi T, Yasuoka K, Willow SY, Fujikawa S, Zeng XC. Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study. J Chem Theory Comput 2013; 9:2540-51. [PMID: 26583851 DOI: 10.1021/ct3010968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have designed various nanoslit systems, whose opposing surfaces can be either hydrophobic, hydrophilic, or simply a water-vapor interface, for the molecular dynamics simulation of confined water with three different protein denaturants, i.e., urea, guanidinium chloride (GdmCl), and methanol, respectively. Particular attention is placed on the preferential adsorption of the denaturant molecules onto the opposing surfaces and associated resident time in the vicinal layer next to the surfaces, as well as their implication in the denaturing efficiency of different denaturant molecules. Our simulation results show that among the three denaturants, the occupancy of methanol in the vicinal layer is the highest while the residence time of Gdm is the longest. Although the occupancy and the residence time of urea in the vicinal layer is less than those of the other two denaturant molecules, urea entails "all-around" properties for being a highly effective denaturant. The distinct characteristics of three denaturants may suggest a different molecular mechanism for the protein denaturation. This comparative simulation by design allows us to gain additional insights, on the molecular level, into the denaturation effect and related hydrophobic effect.
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Affiliation(s)
- Takahiro Koishi
- Department of Applied Physics, University of Fukui, 3-9-1 Bunkyo,Fukui 910-8507, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Soohaeng Yoo Willow
- Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, South Korea
| | - Shigenori Fujikawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
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41
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Das P, Xia Z, Zhou R. Collapse of a hydrophobic polymer in a mixture of denaturants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4877-4882. [PMID: 23517381 DOI: 10.1021/la3046252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The solvent quality of an aqueous mixture of two good solvents, urea and guanidinium chloride (GdmCl), for a hydrophobic polymer was investigated using atomistic molecular dynamics simulations. A counterintuitive collapse of the polymer was found, suggesting that mixing the two denaturants reduces the solvent quality. This cononsolvency of the polymer in the urea + GdmCl mixture is found to be caused by the preferential adsorption of urea on the polymer. The polymer collapses as a result of indirect long-range interactions between monomers resulting from the presence of urea clouds surrounding them. Surprisingly, urea behaves as the better solvent in the mixture not because there exists a stronger affinity of the polymer for urea. Instead, attractive interactions between two unlike denaturant molecules combined with the direct dispersion interactions of the polymer with both denaturants determine the solvent quality of the mixture.
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Affiliation(s)
- Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.
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42
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Heyda J, Muzdalo A, Dzubiella J. Rationalizing Polymer Swelling and Collapse under Attractive Cosolvent Conditions. Macromolecules 2013. [DOI: 10.1021/ma302320y] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Heyda
- Soft Matter
and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109
Berlin, Germany, and Department of Physics, Humboldt-University Berlin, Newtonstr. 15, 12489 Berlin, Germany
| | - Anja Muzdalo
- Soft Matter
and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109
Berlin, Germany, and Department of Physics, Humboldt-University Berlin, Newtonstr. 15, 12489 Berlin, Germany
| | - Joachim Dzubiella
- Soft Matter
and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109
Berlin, Germany, and Department of Physics, Humboldt-University Berlin, Newtonstr. 15, 12489 Berlin, Germany
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43
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Hunger J, Neueder R, Buchner R, Apelblat A. A Conductance Study of Guanidinium Chloride, Thiocyanate, Sulfate, and Carbonate in Dilute Aqueous Solutions: Ion-Association and Carbonate Hydrolysis Effects. J Phys Chem B 2013; 117:615-22. [DOI: 10.1021/jp311425v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Johannes Hunger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Roland Neueder
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Alexander Apelblat
- Department of Chemical
Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
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44
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Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. J Am Chem Soc 2012; 134:18266-74. [PMID: 23057830 DOI: 10.1021/ja3031505] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Both urea and guanidinium chloride (GdmCl) are frequently used as protein denaturants. Given that proteins generally adopt extended or unfolded conformations in either aqueous urea or GdmCl, one might expect that the unfolded protein chains will remain or become further extended due to the addition of another denaturant. However, a collapse of denatured proteins is revealed using atomistic molecular dynamics simulations when a mixture of denaturants is used. Both hen egg-white lysozyme and protein L are found to undergo collapse in the denaturant mixture. The collapse of the protein conformational ensembles is accompanied by a decreased solubility and increased non-native self-interactions of hydrophobic residues in the urea/GdmCl mixture. The increase of non-native interactions rather than the native contacts indicates that the proteins experience a simple collapse transition from the fully denatured states. During the protein collapse, the relatively stronger denaturant GdmCl displays a higher tendency to be absorbed onto the protein surface due to their stronger electrostatic interactions with proteins. At the same time, urea molecules also accumulate near the protein surface, resulting in an enhanced "local crowding" for the protein near its first solvation shell. This rearrangement of denaturants near the protein surface and crowded local environment induce the protein collapse, mainly by burying their hydrophobic residues. These findings from molecular simulations are then further explained by a simple analytical model based on statistical mechanics.
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Affiliation(s)
- Zhen Xia
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
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45
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Shao Q, Fan Y, Yang L, Gao YQ. Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein. J Chem Theory Comput 2012; 8:4364-73. [DOI: 10.1021/ct3002267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Qiang Shao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
- Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203,
China
| | - Yubo Fan
- Bioinformatics and
Bioengineering
Program, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, Texas 77030, United
States
| | - Lijiang Yang
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and
Computational Chemistry, College of Chemistry and Molecular Engineering,
Beijing National Laboratory of Molecular Sciences, Peking University, Beijing 100871, China
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46
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Ou S, Patel S, Bauer BA. Free energetics of carbon nanotube association in pure and aqueous ionic solutions. J Phys Chem B 2012; 116:8154-68. [PMID: 22780909 PMCID: PMC3562760 DOI: 10.1021/jp3025717] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Carbon nanotubes are a promising platform across a broad spectrum of applications ranging from separations technology, drug delivery, to bio(electronic) sensors. Proper dispersion of carbon nanotube materials is important to retaining the electronic properties of nanotubes. Experimentally it has been shown that salts can regulate the dispersing properties of CNTs in aqueous system with surfactants (Niyogi, S.; Densmore, C. G.; Doorn, S. K. J. Am. Chem. Soc.2009, 131, 1144-1153); details of the physicochemical mechanisms underlying such effects continue to be explored. We address the effects of inorganic monovalent salts (NaCl and NaI) on dispersion stability of carbon nanotubes.We perform all-atom molecular dynamics simulations using nonpolarizable interaction models to compute the potential of mean force between two (10,10) single-walled carbon nanotubes (SWNTs) in the presence of NaCl/NaI and compare to the potential of mean force between SWNTs in pure water. Addition of salts enhances stability of the contact state between two SWNT's on the order of 4 kcal/mol. The ion-specific spatial distribution of different halide anions gives rise to starkly different contributions to the free energy stability of nanotubes in the contact state. Iodide anion directly stabilizes the contact state to a much greater extent than chloride anion. The enhanced stability arises from the locally repulsive forces imposed on nanotubes by the surface-segregated iodide anion. Within the time scale of our simulations, both NaI and NaCl solutions stabilize the contact state by equivalent amounts. The marginally higher stability for contact state in salt solutions recapitulates results for small hydrophobic solutes in NaCl solutions (Athawale, M. V.; Sarupria, S.; Garde, S. J. Phys. Chem. B2008, 112, 5661-5670) as well as single-walled carbon nanotubes in NaCl and CaCl2 aqueous solutions.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Physical and Biological Sciences, The College of Saint Rose, Albany, New York 12203, USA
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47
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Jamadagni SN, Godawat R, Garde S. Hydrophobicity of proteins and interfaces: insights from density fluctuations. Annu Rev Chem Biomol Eng 2012; 2:147-71. [PMID: 22432614 DOI: 10.1146/annurev-chembioeng-061010-114156] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Macroscopic characterizations of hydrophobicity (e.g., contact angle measurements) do not extend to the surfaces of proteins and nanoparticles. Molecular measures of hydrophobicity of such surfaces need to account for the behavior of hydration water. Theory and state-of-the-art simulations suggest that water density fluctuations provide such a measure; fluctuations are enhanced near hydrophobic surfaces and quenched with increasing surface hydrophilicity. Fluctuations affect conformational equilibria and dynamics of molecules at interfaces. Enhanced fluctuations are reflected in enhanced cavity formation, more favorable binding of hydrophobic solutes, increased compressibility of hydration water, and enhanced water-water correlations at hydrophobic surfaces. These density fluctuation-based measures can be used to develop practical methods to map the hydrophobicity/philicity of heterogeneous surfaces including those of proteins. They highlight that the hydrophobicity of a group is context dependent and is significantly affected by its environment (e.g., chemistry and topography) and especially by confinement. The ability to include information about hydration water in mapping hydrophobicity is expected to significantly impact our understanding of protein-protein interactions as well as improve drug design and discovery methods and bioseparation processes.
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Affiliation(s)
- Sumanth N Jamadagni
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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48
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Das P. Effect of cosolvents on nano-confined water: a molecular dynamics study. NANOSCALE 2012; 4:2931-2936. [PMID: 22441726 DOI: 10.1039/c2nr30070b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present results from atomistic molecular dynamics simulations to characterize the effects of cosolvents, such as urea and guanidinium (Gdm) salts, on the water confined in hydrophobic carbon nanotubes. We observed complete drying of the nanotube interiors of diameter ranging from 8 to 17 Å in urea. In contrast, the water population within nanotube cores smaller than 12 Å remains unaffected in GdmCl solution, whereas larger nanotube interiors become partially dehydrated with prevailing presence of stable Gdm(+)-Gdm(+) dimers. The molecular arrangement and the lifetime inside the nanotube were found to be characteristics of a particular cosolvent. In both urea and GdmCl solutions, preferential cosolvent intrusion resulting in nanotube dehydration is driven by the stronger dispersion interaction of cosolvent than water with the nanotube. The partial drying of the hydrophobic core is attributed to guanidinium's better hydration and weaker self-association propensity compared to urea, as well as to its moderate ion-pairing with strongly hydrated chloride ions. The Gdm(+) induced dehydration varies with the charge density of counter-ions, as the presence of high charge-density sulfate ions impedes penetration of guanidinium, and consequent dehydration of the nanotube. These findings provide important insights into the effect of cosolvents on the nano-confined water in a hydrophobic environment.
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Affiliation(s)
- Payel Das
- IBM T.J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.
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49
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50
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Crevenna A, Naredi-Rainer N, Lamb D, Wedlich-Söldner R, Dzubiella J. Effects of Hofmeister ions on the α-helical structure of proteins. Biophys J 2012; 102:907-15. [PMID: 22385862 PMCID: PMC3283803 DOI: 10.1016/j.bpj.2012.01.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/15/2011] [Accepted: 01/11/2012] [Indexed: 01/20/2023] Open
Abstract
The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO(4) in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO(4) originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO(4) denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.
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Affiliation(s)
- Alvaro H. Crevenna
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nikolaus Naredi-Rainer
- Physical Chemistry, Department for Chemistry and Biochemistry and Center for Nano Science (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Don C. Lamb
- Physical Chemistry, Department for Chemistry and Biochemistry and Center for Nano Science (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Roland Wedlich-Söldner
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Joachim Dzubiella
- Physics Department T37, Technische Universität München, Garching, Germany
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Berlin, Germany
- Institut für Physik, Humboldt-Universität zu Berlin, Berlin, Germany
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