1
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Nakata N, Okamoto R, Sumi T, Koga K, Morita T, Imamura H. Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein. Protein Sci 2023; 32:e4763. [PMID: 37622187 PMCID: PMC10519159 DOI: 10.1002/pro.4763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.
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Affiliation(s)
- Noa Nakata
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
| | - Ryuichi Okamoto
- Graduate School of Information Science, University of HyogoKobeHyogoJapan
| | - Tomonari Sumi
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Kenichiro Koga
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Takeshi Morita
- Department of ChemistryGraduate School of Science, Chiba UniversityChibaJapan
| | - Hiroshi Imamura
- Department of Bio‐ScienceNagahama Institute of Bio‐Science and TechnologyNagahamaShigaJapan
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2
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Khan S, Khan M, Lohani M, Ahmad S, Sherwani S, Bhagwath S, Khan MWA, Wahid M, Aqil F, Haque S. NADP/H binding nearly doubles the stability of a Mycobacterium drug target: an unfolding study. J Biomol Struct Dyn 2023; 41:8018-8025. [PMID: 36166625 DOI: 10.1080/07391102.2022.2127910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
Mycobacterium Aspartate beta semialdehyde dehydrogenase (ASADH) was studied using various spectroscopic techniques and size exclusion chromatography to examine the unfolding of free (apo) and NADP/H-bound (holo) forms of ASADH. Non-cooperative guanidinium chloride (GdnHCl)-induced unfolding of the apo ASADH was discovered, and no partially folded intermediate structures were stabilized. On the other hand, it was observed that GdnHCl's unfolding of holoenzyme was a cooperative process without any stable intermediate structure. The native form of holoenzyme is found to be stable against the lower concentration of GdnHCl only (namely up to 1.25 M GdnHCl). The tryptophan environment appears to unfold cooperatively in case of the holoenzyme and is in well coordination with the overall unfolding of the holoenzyme. The presence of NADP/H shows a stabilizing effect on the tryptophan environment as well as on the native NADP/H-bound enzyme. Δ G Solvent o values reveal nearly two-fold (∼1.9) conformationally more stable folded holoenzyme compared to its native apo state. The Cm for the apo and holo forms of ASADH are 1.3 and 1.9 M, respectively. Novel drug leads targeting the NADP/H binding domain of ASADH could offer promising drugs against extremely infective Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mahvish Khan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saheem Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Subuhi Sherwani
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Sundeep Bhagwath
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Mohd Wajid A Khan
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farrukh Aqil
- Department of Medicine and James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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3
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Nordquist EB, Schultz SA, Chen J. Using Metadynamics To Explore the Free Energy of Dewetting in Biologically Relevant Nanopores. J Phys Chem B 2022; 126:6428-6437. [PMID: 35998613 PMCID: PMC9932947 DOI: 10.1021/acs.jpcb.2c04157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Water confined within hydrophobic spaces can undergo cooperative dewetting transitions due to slight changes in water density and pressure that push water toward the vapor phase. Many transmembrane protein ion channels contain nanoscale hydrophobic pores that could undergo dewetting transitions, sometimes blocking the flow of ions without physical blockages. Standard molecular dynamics simulations have been extensively applied to study the behavior of water in nanoscale pores, but the large free energy barriers of dewetting often prevent direct sampling of both wet and dry states and quantitative studies of the hydration thermodynamics of biologically relevant pores. Here, we describe a metadynamics protocol that uses the number of waters within the pore as the collective variable to drive many reversible transitions between relevant hydration states and calculate well-converged free energy profiles of pore hydration. By creating model nanopore systems and changing their radius and morphology and including various cosolvents, we quantify how these pore properties and cosolvents affect the dewetting transition. The results reveal that the dewetting free energy of nanoscale pores is determined by two key thermodynamic parameters, namely, the effective surface tension coefficients of water-air and water-pore interfaces. Importantly, while the effect of salt can be fully captured in the water activity dependence, amphipathic cosolvents such as alcohols modify both dry and wet states of the pore and dramatically shift the wet-dry equilibrium. The metadynamics approach could be applied to studies of dewetting transitions within nanoscale pores of proteins and provide new insights into why different pore properties evolved in biological systems.
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Affiliation(s)
- Erik B. Nordquist
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Samantha A. Schultz
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst Massachusetts, USA 01003
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst Massachusetts, USA 01003
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4
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Kovács A, Yusupov M, Cornet I, Billen P, Neyts EC. Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Sundar S, Sandilya AA, Priya MH. Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis. J Chem Inf Model 2021; 61:3927-3944. [PMID: 34379415 DOI: 10.1021/acs.jcim.1c00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water structure in aqueous osmolyte solutions, deduced from the slight alteration in the water-water radial distribution function, the decrease in water-water hydrogen bonding, and tetrahedral ordering based only on the orientation of nearest water molecules derived from the molecular dynamics simulations, appears to have been perturbed. A careful analysis, however, reveals that the hydrogen bonding and the tetrahedral ordering around a water molecule in binary solutions remain intact as in neat water when the contribution of osmolyte-water interactions is appropriately incorporated. Furthermore, the distribution of the water binding energies and the water excess chemical potential of solvation in solutions are also pretty much the same as in neat water. Osmolytes are, therefore, well integrated into the hydrogen-bond network of water. Indeed, osmolytes tend to preferentially hydrogen bond with water molecules and their interaction energies are strongly correlated to their hydrogen-bonding capability. The graph network analysis, further, illustrates that osmolytes act as hubs in the percolated hydrogen-bond network of solutions. The degree of hydrogen bonding of osmolytes predominantly determines all of the network properties. Osmolytes like ethanol that form fewer hydrogen bonds than a water molecule disrupt the water hydrogen-bond network, while other osmolytes that form more hydrogen bonds effectively increase the connectivity among water molecules. Our observation of minimal variation in the local structure and the vitality of osmolyte-water hydrogen bonds on the solution network properties clearly imply that the direct interaction between protein and osmolytes is solely responsible for the protein stability. Further, the relevance of hydrogen bonds on solution properties suggests that the hydrogen-bonding interaction among protein, water, and osmolyte could be the key determinant of the protein conformation in solutions.
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Affiliation(s)
- Smrithi Sundar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Avilasha A Sandilya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Hamsa Priya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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6
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7
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Dilip.H.N., Chakraborty D. Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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8
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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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9
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Abstract
SummaryNutrition influences the microenvironment in the proximity of oocyte and affects early embryonic development. Elevated blood urea nitrogen, even in healthy dairy cows, is associated with reduced fertility and there is high correlation between blood urea levels and follicular fluid urea levels. Using a docking calculation (in silico), urea showed a favorable binding activity towards the ZP-N domain of ZP3, that of ZP2, and towards the predicted full-length sperm receptor ZP3. Supplementation of oocyte maturation medium with nutrition-related levels of urea (20 or 40 mg/dl as seen in healthy dairy cows fed on low or high dietary protein, respectively) dose-dependently increased: (i) the proportion of oocytes that remained uncleaved; and (ii) oocyte degeneration; and reduced cleavage, blastocyst and hatching rates. High levels of urea induced shrinkage in oocytes, visualised using scanning electron microscopy. Urea downregulated NANOG while dose-dependently upregulating OCT4, DNMT1, and BCL2 expression. Urea at 20 mg/dl induced BAX expression. Using mathematical modelling, the rate of oocyte degeneration was sensitive to urea levels; while cleavage, blastocyst and hatching rates exhibited negative sensitivity. The present data imply a novel role for urea in reducing oocyte competence and changing gene expression in the resultant embryos.
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10
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Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem 2018; 542:40-57. [DOI: 10.1016/j.ab.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
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11
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Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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12
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Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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13
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Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation. Sci Rep 2016; 6:32277. [PMID: 27573790 PMCID: PMC5004150 DOI: 10.1038/srep32277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023] Open
Abstract
Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both 'direct' and 'indirect' mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.
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14
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Ferreira LA, Povarova OI, Stepanenko OV, Sulatskaya AI, Madeira PP, Kuznetsova IM, Turoverov KK, Uversky VN, Zaslavsky BY. Effects of low urea concentrations on protein-water interactions. J Biomol Struct Dyn 2016; 35:207-218. [DOI: 10.1080/07391102.2015.1135823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luisa A. Ferreira
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA
| | - Olga I. Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Pedro P. Madeira
- Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, Porto 4200-465, Portugal
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biophysics, St. Petersburg State Polytechnic University, St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA
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15
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Yamamori Y, Ishizuka R, Karino Y, Sakuraba S, Matubayasi N. Interaction-component analysis of the hydration and urea effects on cytochrome c. J Chem Phys 2016; 144:085102. [DOI: 10.1063/1.4941945] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yasuhito Karino
- RIKEN Quantitative Biology Center, Kobe, Hyogo 650-0047, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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16
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Moore KE, Mangos DN, Slattery AD, Raston CL, Boulos RA. Wool deconstruction using a benign eutectic melt. RSC Adv 2016. [DOI: 10.1039/c5ra26516a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Wool fibre is deconstructed in a facile ‘top down’ fabrication process into functional, nano-dimensional α-keratin chains using a benign choline chloride-urea deep eutectic solvent (DES) melt.
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Affiliation(s)
- Katherine E. Moore
- Centre for NanoScale Science and Technology
- School of Chemical and Physical Science
- Flinders University
- Australia
| | - Daniel N. Mangos
- Centre for NanoScale Science and Technology
- School of Chemical and Physical Science
- Flinders University
- Australia
- The International Musculoskeletal Research Institute
| | - Ashley D. Slattery
- Centre for NanoScale Science and Technology
- School of Chemical and Physical Science
- Flinders University
- Australia
| | - Colin L. Raston
- Centre for NanoScale Science and Technology
- School of Chemical and Physical Science
- Flinders University
- Australia
| | - Ramiz A. Boulos
- Centre for NanoScale Science and Technology
- School of Chemical and Physical Science
- Flinders University
- Australia
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17
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Minkara MS, Weaver MN, Merz KM. Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study. Biochemistry 2015; 54:4121-30. [DOI: 10.1021/acs.biochem.5b00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mona S. Minkara
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
| | - Michael N. Weaver
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East
Lansing, Michigan 48824-1322, United States
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18
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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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19
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Roy S, Bagchi B. Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting. J Phys Chem B 2014; 118:5691-7. [DOI: 10.1021/jp5037348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Susmita Roy
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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20
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Ható Z, Makó É, Kristóf T. Water-mediated potassium acetate intercalation in kaolinite as revealed by molecular simulation. J Mol Model 2014; 20:2140. [PMID: 24549796 DOI: 10.1007/s00894-014-2140-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/01/2014] [Indexed: 10/25/2022]
Abstract
Molecular simulations are suitable tools to study the adsorption and intercalation of molecules in clays. In this work, a recently proposed thermodynamically consistent force field for inorganic compounds (INTERFACE, Heinz H, Lin TJ, Mishra RK, Emami FS (2013) Langmuir 29:1754-1765), which enables accurate simulations of inorganic-organic interfaces, was tested for a two-sheet type clay mineral. All-atom NpT molecular dynamics simulations were used to describe the characteristics (basal spacing, loading, molecular orientation) of some intercalate complexes of kaolinite with potassium acetate and the results were compared with the available experimental data. The most probable structural configurations of the kaolinite/potassium acetate intercalate complexes were determined from the simulations. Our examinations confirmed some supposed (single- or double-layered) arrangements of guest molecules. The need of interlayer water in the intercalate complex, which can be produced by the basic synthesis procedure in air atmosphere, was verified.
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Affiliation(s)
- Zoltán Ható
- Institute of Chemistry, Department of Physical Chemistry, University of Pannonia, P.O. Box 158, 8201, Veszprém, Hungary
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21
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Monhemi H, Housaindokht MR, Moosavi-Movahedi AA, Bozorgmehr MR. How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent. Phys Chem Chem Phys 2014; 16:14882-93. [DOI: 10.1039/c4cp00503a] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Mandal M, Mukhopadhyay C. Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin. Phys Chem Chem Phys 2014; 16:21706-16. [DOI: 10.1039/c4cp01657b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.
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Affiliation(s)
- Manoj Mandal
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009, India
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23
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Cai Z, Li J, Yin C, Yang Z, Wu J, Zhou R. Effect of urea concentration on aggregation of amyloidogenic hexapeptides (NFGAIL). J Phys Chem B 2013; 118:48-57. [PMID: 24328094 DOI: 10.1021/jp407776e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have performed large-scale all-atom molecular dynamics (MD) simulations to study the aggregation behavior of four NFGAIL hexapeptides in the aqueous urea solution, with a urea concentration ranging from 0 to 5 M. We find that urea in general suppresses the peptide aggregation, but suppression slows down in the intermediation concentration regime around 3 M. Two competing mechanisms of urea are determined: urea molecules accumulated near the first solvation shell (FSS) tend to unfold the hexapeptide, which favors aggregation; on the other hand, the tight hydrogen bonds formed between urea and peptide mainchains hinder the association of peptides which disfavors the formation of the β-sheet. Furthermore, the different nonlinear urea concentration dependences of the urea-peptide and peptide-peptide hydrogen bonds lead to a nonmonotonic behavior, with a weak enhancement in the peptide aggregation around 3 M.
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Affiliation(s)
- Zhuowei Cai
- Department of Physics, Zhejiang University , Hangzhou, 310027, China
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24
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Yoon J, Thirumalai D, Hyeon C. Urea-induced denaturation of preQ1-riboswitch. J Am Chem Soc 2013; 135:12112-21. [PMID: 23863126 DOI: 10.1021/ja406019s] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urea, a polar molecule with a large dipole moment, not only destabilizes folded RNA structures but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive all-atom molecular dynamics simulations to determine the molecular underpinnings of urea-induced RNA denaturation. Urea displays its denaturing power in both secondary and tertiary motifs of the riboswitch structure. Our simulations reveal that the denaturation of RNA structures is mainly driven by the hydrogen-bonding and stacking interactions of urea with the bases. Through detailed studies of the simulation trajectories, we found that geminate pairs between urea and bases due to hydrogen bonds and stacks persist only ~0.1-1 ns, which suggests that the urea-base interaction is highly dynamic. Most importantly, the early stage of base-pair disruption is triggered by penetration of water molecules into the hydrophobic domain between the RNA bases. The infiltration of water into the narrow space between base pairs is critical in increasing the accessibility of urea to transiently disrupted bases, thus allowing urea to displace inter-base hydrogen bonds. This mechanism--water-induced disruption of base pairs resulting in the formation of a "wet" destabilized RNA followed by solvation by urea--is the exact opposite of the two-stage denaturation of proteins by urea. In the latter case, initial urea penetration creates a dry globule, which is subsequently solvated by water, leading to global protein unfolding. Our work shows that the ability to interact with both water and polar or nonpolar components of nucleotides makes urea a powerful chemical denaturant for nucleic acids.
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Affiliation(s)
- Jeseong Yoon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea
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25
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The effects of urea, guanidinium chloride and sorbitol on porphyrin aggregation: Molecular dynamics simulation. J CHEM SCI 2013. [DOI: 10.1007/s12039-013-0411-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Karino Y, Matubayasi N. Interaction-component analysis of the urea effect on amino acid analogs. Phys Chem Chem Phys 2013; 15:4377-91. [DOI: 10.1039/c3cp43346c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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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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28
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Kleinjung J, Fraternali F. Urea-Water Solvation Forces on Prion Structures. J Chem Theory Comput 2012; 8:3977-3984. [PMID: 23066353 PMCID: PMC3466777 DOI: 10.1021/ct300264w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 01/28/2023]
Abstract
Solvation forces are crucial determinants in the equilibrium between the folded and unfolded state of proteins. Particularly interesting are the solvent forces of denaturing solvent mixtures on folded and misfolded states of proteins involved in neurodegeneration. The C-terminal globular domain of the ovine prion protein (1UW3) and its analogue H2H3 in the α-rich and β-rich conformation were used as model structures to study the solvation forces in 4 M aqueous urea using molecular dynamics. The model structures display very different secondary structures and solvent exposures. Most protein atoms favor interactions with urea over interactions with water. The force difference between protein-urea and protein-water interactions correlates with hydrophobicity; i.e., urea interacts preferentially with hydrophobic atoms, in agreement with results from solvent transfer experiments. Solvent Shannon entropy maps illustrate the mobility gradient of the urea-water mixture from the first solvation shell to the bulk. Single urea molecules replace water in the first solvation shell preferably at locations of relatively high solvent entropy.
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Affiliation(s)
- Jens Kleinjung
- Division of Mathematical Biology,
MRC National Institute for Medical Research, The Ridgeway, Mill Hill,
London NW7 1AA, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and
Molecular Biophysics, King’s College London, New Hunt’s
House, London SE1 1UL, United Kingdom
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29
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Yang Z, Xiu P, Shi B, Hua L, Zhou R. Coherent microscopic picture for urea-induced denaturation of proteins. J Phys Chem B 2012; 116:8856-62. [PMID: 22780326 DOI: 10.1021/jp304114h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In a previous study, we explored the mechanism of urea-induced denaturation of proteins by performing molecular dynamics (MD) simulations of hen lysozyme in 8 M urea and supported the "direct interaction mechanism" whereby urea denatures protein via dispersion interaction (Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16928). Here we perform large scale MD simulations of five representative protein/peptide systems in aqueous urea to investigate if the above mechanism is common to other proteins. In all cases, accumulations of urea around proteins/peptide are observed, suggesting that urea denatures proteins by directly attacking protein backbones and side chains rather than indirectly disrupting water structure as a "water breaker". Consistent with our previous case study of lysozyme, the current energetic analyses with five protein/peptide systems reveal that urea's preferential binding to proteins mainly comes from urea's stronger dispersion interactions with proteins than with bulk solution, whereas the electrostatic (hydrogen-bonded) interactions only play a relatively minor (even negative) role during this denaturation process. Furthermore, the simulations of the peptide system at different urea concentrations (8 and 4.5 M), and with different force fields (CHARMM and OPLSAA) suggest that the above mechanism is robust, independent of the urea concentration and force field used. Last, we emphasize the importance of periodic boundary conditions in pairwise energetic analyses. This article provides a comprehensive study on the physical mechanism of urea-induced protein denaturation and suggests that the "dispersion-interaction-driven" mechanism should be general.
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Affiliation(s)
- Zaixing Yang
- Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
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30
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Levin EJ, Cao Y, Enkavi G, Quick M, Pan Y, Tajkhorshid E, Zhou M. Structure and permeation mechanism of a mammalian urea transporter. Proc Natl Acad Sci U S A 2012; 109:11194-9. [PMID: 22733730 PMCID: PMC3396522 DOI: 10.1073/pnas.1207362109] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As an adaptation to infrequent access to water, terrestrial mammals produce urine that is hyperosmotic to plasma. To prevent osmotic diuresis by the large quantity of urea generated by protein catabolism, the kidney epithelia contain facilitative urea transporters (UTs) that allow rapid equilibration between the urinary space and the hyperosmotic interstitium. Here we report the first X-ray crystal structure of a mammalian UT, UT-B, at a resolution of 2.36 Å. UT-B is a homotrimer and each protomer contains a urea conduction pore with a narrow selectivity filter. Structural analyses and molecular dynamics simulations showed that the selectivity filter has two urea binding sites separated by an approximately 5.0 kcal/mol energy barrier. Functional studies showed that the rate of urea conduction in UT-B is increased by hypoosmotic stress, and that the site of osmoregulation coincides with the location of the energy barrier.
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Affiliation(s)
- Elena J. Levin
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Yu Cao
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Giray Enkavi
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; and
| | - Matthias Quick
- Department of Psychiatry and Center for Molecular Recognition, Columbia University, 650 West 168th Street, New York, NY 10032
| | - Yaping Pan
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032
| | - Emad Tajkhorshid
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; and
| | - Ming Zhou
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032
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31
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Wang Q, Christiansen A, Samiotakis A, Wittung-Stafshede P, Cheung MS. Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II. J Chem Phys 2012; 135:175102. [PMID: 22070324 DOI: 10.1063/1.3656692] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature T(b) and chemical denaturation at another temperature T(u) using the stability change of a protein (ΔG). For this, we related the dependence of ΔG on temperature, in the Gibbs-Helmholtz equation, to that of ΔG on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (T(u)) and the aqueous (T(b)) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, T(b), and the temperature of the same structural ensemble at a specific urea concentration, T(u). The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.
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Affiliation(s)
- Qian Wang
- Department of Physics, University of Houston, Houston, Texas 77204-5005, USA
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32
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Huang JR, Gabel F, Jensen MR, Grzesiek S, Blackledge M. Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering data. J Am Chem Soc 2012; 134:4429-36. [PMID: 22309138 DOI: 10.1021/ja2118688] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular details of how urea interacts with, and eventually denatures proteins, remain largely unknown. In this study we have used extensive experimental NMR data, in combination with statistical coil ensemble modeling and small-angle scattering, to analyze the conformational behavior of the protein ubiquitin in the presence of urea. In order to develop an atomic resolution understanding of the denatured state, conformational ensembles of full-atom descriptions of unfolded proteins, including side chain conformations derived from rotamer libraries, are combined with random sampling of explicit urea molecules in interaction with the protein. Using this description of the conformational equilibrium, we demonstrate that the direct-binding model of urea to the protein backbone is compatible with available experimental data. We find that, in the presence of 8 M urea, between 30 and 40% of the backbone peptide groups bind a urea molecule, independently reproducing results from a model-free analysis of small-angle neutron and X-ray scattering data. Crucially, this analysis also provides sequence specific details of the interaction between urea and the protein backbone. The pattern of urea-binding along the amino-acid sequence reveals a higher level of binding in the central part of the protein, a trend which resembles independent results derived from chemical shift mapping of the urea-protein interaction. Together these results substantiate the direct-binding model and provide a framework for studying the physical basis of interactions between proteins and solvent molecules.
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Affiliation(s)
- Jie-rong Huang
- CEA, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France
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33
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Li W, Mu Y. Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: a molecular dynamics study. NANOSCALE 2012; 4:1154-1159. [PMID: 22105862 DOI: 10.1039/c1nr11108f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It has been a long history that urea and guanidinium chloride (GdmCl) are used as agents for denaturing proteins. The underlying mechanism has been extensively studied in the past several decades. However, the question regarding why GdmCl is much stronger than urea has seldom been touched. Here, through molecular dynamics simulations, we show that a 4 M GdmCl solution is more able than 7 M urea solution to dissociate both hydrophobic and charged nano-particles (NP). Both urea and GdmCl affect the NPs' aggregation through direct binding to the NP surface. The advantages of GdmCl originate from the net charge of bound guanidinium ions which can generate a local positively charged environment around hydrophobic and negatively charged NPs. This effective coating can introduce Coulombic repulsion between all the NPs. Urea shows certain ability to dissociate hydrophobic NPs. However, in the case of charged NPs, urea molecules located between two opposite-charged NPs will form ordered hydrogen bonds, acting like "glue" which prevents separation of the NPs. Although urea can form hydrogen bonds with either hydrophilic amino acids or the protein backbone, which are believed to contribute to protein denaturation, our findings strongly suggest that this property does not always contribute positively to urea's denaturation power.
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Affiliation(s)
- Weifeng Li
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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34
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Haldar S, Chattopadhyay K. Interconnection of salt-induced hydrophobic compaction and secondary structure formation depends on solution conditions: revisiting early events of protein folding at single molecule resolution. J Biol Chem 2012; 287:11546-55. [PMID: 22303014 DOI: 10.1074/jbc.m111.315648] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea.
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Affiliation(s)
- Shubhasis Haldar
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council for Scientific and Industrial Research, 4 Raja S.C. Mullick Rd., Kolkata 700032, India
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35
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Toofanny RD, Daggett V. Understanding protein unfolding from molecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rudesh D. Toofanny
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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36
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Sengupta A, Khade RV, Hazra P. How Does the Urea Dynamics Differ from Water Dynamics inside the Reverse Micelle? J Phys Chem A 2011; 115:10398-407. [DOI: 10.1021/jp206069z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abhigyan Sengupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
| | - Rahul V. Khade
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411021, Maharashtra, India
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37
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Eberini I, Emerson A, Sensi C, Ragona L, Ricchiuto P, Pedretti A, Gianazza E, Tramontano A. Simulation of urea-induced protein unfolding: A lesson from bovine β-lactoglobulin. J Mol Graph Model 2011; 30:24-30. [DOI: 10.1016/j.jmgm.2011.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 01/16/2023]
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38
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Xue Y, Skrynnikov NR. Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? J Am Chem Soc 2011; 133:14614-28. [PMID: 21819149 DOI: 10.1021/ja201605c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics (MD) simulations have been widely used to analyze dynamic conformational equilibria of folded proteins, especially in relation to NMR observables. However, this approach found little use in the studies of disordered proteins, where the sampling of vast conformational space presents a serious problem. In this paper, we demonstrate that the latest advances in computation technology make it possible to overcome this limitation. The experimentally validated (calibrated) MD models allow for new insights into structure/dynamics of disordered proteins. As a test system, we have chosen denatured ubiquitin in solution with 8 M urea at pH 2. High-temperature MD simulations in implicit solvent have been carried out for the wild-type ubiquitin as well as MTSL-tagged Q2C, D32C, and R74C mutants. To recalibrate the MD data (500 K) in relation to the experimental conditions (278 K, 8 M urea), the time axes of the MD trajectories were rescaled. The scaling factor was adjusted such as to maximize the agreement between the simulated and experimental (15)N relaxation rates. The resulting effective length of the trajectories, 311 μs, ensures good convergence properties of the MD model. The constructed MD model was validated against the array of experimental data, including additional (15)N relaxation parameters, multiple sets of paramagnetic relaxation enhancements (PREs), and the radius of gyration. In each case, a near-quantitative agreement has been obtained, suggesting that the model is successful. Of note, the MD-based approach rigorously predicts the quantities that are inherently dynamic, i.e., dependent on the motional correlation times. This cannot be accomplished, other than in empirical fashion, on the basis of static structural models (conformational ensembles). The MD model was further used to investigate the relative translational motion of the MTSL label and the individual H(N) atoms. The derived segmental diffusion coefficients proved to be nearly uniform along the peptide chain, averaging to D = 0.49-0.55 × 10(-6) cm(2)/s. This result was verified by direct analysis of the experimental PRE data using the recently proposed Ullman-Podkorytov model. In this model, MTSL and H(N) moieties are treated as two tethered spheres undergoing mutual diffusion in a harmonic potential. The fitting of the experimental data involving D as a single adjustable parameter leads to D = 0.45 × 10(-6) cm(2)/s, in good agreement with the MD-based analyses. This result can be compared with the range of estimates obtained from the resonance energy transfer experiments, D = 0.2-6.0 × 10(-6) cm(2)/s.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, USA
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39
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Mason PE, Lerbret A, Saboungi ML, Neilson GW, Dempsey CE, Brady JW. Glucose interactions with a model peptide. Proteins 2011; 79:2224-32. [PMID: 21574187 DOI: 10.1002/prot.23047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 02/12/2011] [Accepted: 03/03/2011] [Indexed: 11/07/2022]
Abstract
Molecular dynamics simulations have been conducted of the helical polypeptide melittin, in concentrated aqueous solutions of the alpha and beta anomers of D-glucopyranose. Glucose is an osmolyte, and it is expected to be preferentially excluded from the surfaces of proteins. This was indeed found to be the case in the simulations. The results indicate that the observed exclusion may have a contribution from an under-representation of hydrogen bonding interactions between glucose groups and exposed side chains, compared to water. However, glucose was found to bind quite specifically to melittin by stacking its hydrophobic face, consisting of aliphatic protons, against the flat hydrophobic face of the indole group of the tryptophan-19 side chain. Although the binding site for this interaction is localized, the binding is weak for both anomers, with a binding free energy estimated as only ∼0.5 kcal/mol (i.e. near k(B)T). The face of the sugar stacked against the Trp indole ring is different for the two anomers of glucose, due to the disruption of the H1-H3-H5 hydrophobic triad of the beta anomer by the axial C1 hydroxyl group in the alpha anomer. The measurable affinity of the sugar for the Trp side chain is consistent with the very frequent occurrence of this group in the binding sites of proteins that complex with sugars.
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Affiliation(s)
- Phillip E Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
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40
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Xiu P, Yang Z, Zhou B, Das P, Fang H, Zhou R. Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models. J Phys Chem B 2011; 115:2988-94. [DOI: 10.1021/jp108303q] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Peng Xiu
- Bio-X Lab, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Zaixing Yang
- Bio-X Lab, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Bo Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
| | - Haiping Fang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
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41
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Takeda T, Chang WE, Raman EP, Klimov DK. Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril. Proteins 2011; 78:2849-60. [PMID: 20635343 DOI: 10.1002/prot.22804] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonsteroidal anti-inflammatory drugs are considered as potential therapeutic agents against Alzheimer's disease. Using replica exchange molecular dynamics and atomistic implicit solvent model, we studied the mechanisms of binding of naproxen and ibuprofen to the Abeta fibril derived from solid-state NMR measurements. The binding temperature of naproxen is found to be almost 40 K higher than of ibuprofen implicating higher binding affinity of naproxen. The key factor, which enhances naproxen binding, is strong interactions between ligands bound to the surface of the fibril. The naphthalene ring in naproxen appears to provide a dominant contribution to ligand-ligand interactions. In contrast, ligand-fibril interactions cannot explain differences in the binding affinities of naproxen and ibuprofen. The concave fibril edge with the groove is identified as the primary binding location for both ligands. We show that confinement of the ligands to the groove facilitates ligand-ligand interactions that lowers the energy of the ligands bound to the concave edge compared with those bound to the convex edge. Our simulations appear to provide microscopic rationale for the differing binding affinities of naproxen and ibuprofen observed experimentally.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA
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42
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Franca EF, Freitas LCG, Lins RD. Chitosan molecular structure as a function of N-acetylation. Biopolymers 2011; 95:448-60. [PMID: 21328576 DOI: 10.1002/bip.21602] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 11/10/2022]
Abstract
Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with ϕ and ψ values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3-HO3((n)) ···O5((n +) (1)) hydrogen bond, which in turn controls particle aggregation.
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Affiliation(s)
- Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG 38400-902, Brazil
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43
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Kokubo H, Hu CY, Pettitt BM. Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine. J Am Chem Soc 2011; 133:1849-58. [PMID: 21250690 DOI: 10.1021/ja1078128] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nature in which the protecting osmolyte trimethylamine N-oxide (TMAO) and the denaturing osmolyte urea affect protein stability is investigated, simulating a decaalanine peptide model in multiple conformations of the denatured ensemble. Binary solutions of both osmolytes and mixed osmolyte solutions at physiologically relevant concentrations of 2:1 (urea:TMAO) are studied using standard molecular dynamics simulations and solvation free energy calculations. Component analysis reveals the differences in the importance of the van der Waals (vdW) and electrostatic interactions for protecting and denaturing osmolytes. We find that urea denaturation governed by transfer free energy differences is dominated by vdW attractions, whereas TMAO exerts its effect by causing unfavorable electrostatic interactions both in the binary solution and mixed osmolyte solution. Analysis of the results showed no evidence in the ternary solution of disruption of the correlations among the peptide and osmolytes, nor of significant changes in the strength of the water hydrogen bond network.
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Affiliation(s)
- Hironori Kokubo
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, United States
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44
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Zhou R, Li J, Hua L, Yang Z, Berne BJ. Comment on "urea-mediated protein denaturation: a consensus view". J Phys Chem B 2011; 115:1323-6; discussion 1327-8. [PMID: 21247088 DOI: 10.1021/jp105160a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
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45
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Gao M, She ZS, Zhou R. Key Residues that Play a Critical Role in Urea-Induced Lysozyme Unfolding. J Phys Chem B 2010; 114:15687-93. [DOI: 10.1021/jp1052453] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Meng Gao
- College of Engineering, Center for Theoretical Biology, and State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing 100871, China, Department of Chemistry, Columbia University, New York, New York 10027, United States, and Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
| | - Zhen-Su She
- College of Engineering, Center for Theoretical Biology, and State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing 100871, China, Department of Chemistry, Columbia University, New York, New York 10027, United States, and Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
| | - Ruhong Zhou
- College of Engineering, Center for Theoretical Biology, and State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing 100871, China, Department of Chemistry, Columbia University, New York, New York 10027, United States, and Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
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46
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Lindgren M, Westlund PO. The affect of urea on the kinetics of local unfolding processes in chymotrypsin inhibitor 2. Biophys Chem 2010; 151:46-53. [DOI: 10.1016/j.bpc.2010.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 04/18/2010] [Accepted: 05/10/2010] [Indexed: 10/19/2022]
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47
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Hédoux A, Krenzlin S, Paccou L, Guinet Y, Flament MP, Siepmann J. Influence of urea and guanidine hydrochloride on lysozyme stability and thermal denaturation; a correlation between activity, protein dynamics and conformational changes. Phys Chem Chem Phys 2010; 12:13189-96. [PMID: 20820578 DOI: 10.1039/c0cp00602e] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of urea and guanidine hydrochloride (GuHCl) on lysozyme stability has been investigated using activity measurements, microcalorimetry and Raman spectroscopy in the low-frequency and amide I regions. Raman investigations on lysozyme dissolved in H(2)O and D(2)O in the presence of up to 10 M denaturants have revealed direct binding between the protein and both denaturants. The analysis of isotopic exchanges in the amide I region allows the identification of binding sites as hydrophilic and hydrophobic groups, respectively, for urea and GuHCl. The weak loss of activity of lysozyme in the presence of urea (∼15% maximum) is mainly assigned to a transformation of the tertiary structure corresponding to a molten globule state without unfolding of α-helix structures, in contrast to GuHCl which clearly induces conformational changes, associated with a larger loss of activity (40% maximum). The denaturing power of urea and guanidine hydrochloride on lysozyme has been related to the solvent and protein dynamics, reflecting direct interaction between denaturants and protein. It clearly appears that solvent dynamics control protein dynamics, and the significant hardening of the dynamics of GuHCl aqueous solutions is considered responsible for its important denaturing power. The comparison between the low-frequency spectra of solvents and lysozyme aqueous solutions in the absence and presence of different types of additives (urea, GuHCl, trehalose) reveals the Raman signature of the hydration water dynamics. This comparison points out the exclusion of trehalose around the protein surface.
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Affiliation(s)
- Alain Hédoux
- Univ Lille Nord de France, F-59000 Lille, France.
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48
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Hu CY, Kokubo H, Lynch GC, Bolen DW, Pettitt BM. Backbone additivity in the transfer model of protein solvation. Protein Sci 2010; 19:1011-22. [PMID: 20306490 DOI: 10.1002/pro.378] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DeltaG(tr)) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DeltaG(tr) values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of -54 cal/mol/M compares quite favorably with -43 cal/mol/M determined experimentally.
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Affiliation(s)
- Char Y Hu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
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49
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Ma L, Liu C, Huang A, Liao D, Yang H, He W, Wei Q. Conformational Stability of Bovine Serum Albumin in Aqueous Amides: A Further Insight into the Mechanism of Urea Acting on the Protein. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Ma L, Pegram L, Record MT, Cui Q. Preferential interactions between small solutes and the protein backbone: a computational analysis. Biochemistry 2010; 49:1954-62. [PMID: 20121154 DOI: 10.1021/bi9020082] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To improve our understanding of the effects of small solutes on protein stability, we conducted atomistic simulations to quantitatively characterize the interactions between two broadly used small solutes, urea and glycine betaine (GB), and a triglycine peptide, which is a good model for a protein backbone. Multiple solute concentrations were analyzed, and each solute-peptide-water ternary system was studied with approximately 200-300 ns of molecular dynamics simulations with the CHARMM force field. The comparison between calculated preferential interaction coefficients (Gamma(23)) and experimentally measured values suggests that semiquantitative agreement with experiments can be obtained if care is exercised to balance interactions among the solute, protein, and water. On the other hand, qualitatively incorrect (i.e., wrong sign in Gamma(23)) results can be obtained if a solute model is constructed by directly taking parameters for chemically similar groups from an existing force field. Such sensitivity suggests that small solute thermodynamic data can be valuable in the development of accurate force field models of biomolecules. Further decomposition of Gamma(23) into group contributions leads to additional insights regarding the effects of small solutes on protein stability. For example, use of the CHARMM force field predicts that urea preferentially interacts with not only amide groups in the peptide backbone but also aliphatic groups, suggesting a role for these interactions in urea-induced protein denaturation; quantitatively, however, it is likely that the CHARMM force field overestimates the interaction between urea and aliphatic groups. The results with GB support a simple thermodynamic model that assumes additivity of preferential interaction between GB and various biomolecular surfaces.
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Affiliation(s)
- Liang Ma
- Graduate Program in Biophysics and Department of Chemistry, University of Wisconsin, University Avenue, Madison, Wisconsin 53706, USA
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