Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation
10.1371/journal.pcbi.1000221
Crossref journal-article
Public Library of Science (PLoS)
PLoS Computational Biology (340)
Bibliography

Stumpe, M. C., & Grubmüller, H. (2008). Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation. PLoS Computational Biology, 4(11), e1000221.

Authors 2
  1. Martin C. Stumpe (first)
  2. Helmut Grubmüller (additional)
References 66 Referenced 65
  1. 10.1021/j100789a503 / J Phys Chem / The effect of urea and amides upon water structure. by JA Rupley (1964)
  2. 10.1063/1.1668057 / J Chem Phys / Structural approach to the solvent power of water for hydrocarbons; urea as a structure breaker. by HS Frank (1968)
  3. 10.1021/ja981529n / J Am Chem Soc / Effect of the protein denaturants urea and guanidinium on water structure: a structural and thermodynamic study. by F Vanzi (1998)
  4. 10.1016/S0021-9258(18)51830-5 / J Biol Chem / Solubility of amino acids and related compounds in aqueous urea solutions. by Y Nozaki (1963)
  5. 10.1021/ja01089a028 / J Am Chem Soc / The effect of compounds of the urea-guanidinium class on the activity coefficient of acetyltetraglycine ethyl ester and related compound. by DR Robinson (1965)
  6. 10.1021/ja00836a027 / J Am Chem Soc / Interactions of urea and other polar compounds in water. by M Roseman (1975)
  7. 10.1063/1.465626 / J Chem Phys / Raman spectroscopic investigation of the dynamics of urea-water complexes. by X Hoccart (1993)
  8. 10.1063/1.481566 / J Chem Phys / A molecular dynamics study of the urea/water mixture. by A Idrissi (2000)
  9. 10.1016/j.saa.2004.02.039 / Spectrochim Acta A / Molecular structure and dynamics of liquids: aqueous urea solutions. by A Idrissi (2005)
  10. 10.1016/S0969-2126(99)80064-1 / Structure / Structural details of urea binding to barnase: a molecular dynamics analysis. by A Caflisch (1999)
  11. 10.1073/pnas.0930122100 / Proc Natl Acad Sci U S A / The molecular basis for the chemical denaturation of proteins by urea. by BJ Bennion (2003)
  12. 10.1529/biophysj.105.061978 / Biophys J / Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization. by A Caballero-Herrera (2005)
  13. 10.1021/jp011462h / J Phys Chem B / Molecular association in solution: a Kirkwood-Buff analysis of sodium chloride, ammonium sulfate, guanidinium chloride, urea, and 2,2,2-trifluoroethanol in water. by R Chitra (2002)
  14. 10.1021/ja039335h / J Am Chem Soc / Impact of protein denaturants and stabilizers on water structure. by JD Batchelor (2004)
  15. 10.1021/j100372a093 / J Phys Chem / A model for the partial reversal of hydrophobic hydration by addition of a urea-like cosolvent. by N Muller (1990)
  16. 10.1021/bi00238a023 / Biochemistry / Solvent denaturation and stabilization of globular proteins. by DOV Alonso (1991)
  17. 10.1016/0022-2836(92)90963-K / J Mol Biol / Protein interactions with urea and guanidinium chloride. A calorimetric study. by GI Makhatadze (1992)
  18. 10.1021/ja00073a050 / J Am Chem Soc / Do denaturants interact with aromatic hydrocarbons in water? by EM Duffy (1993)
  19. 10.1063/1.471686 / J Chem Phys / Keeping the shape but changing the charges: a simulation study of urea and its iso-steric analogs. by J Tsai (1996)
  20. 10.1002/(SICI)1097-0134(19980501)31:2<107::AID-PROT1>3.0.CO;2-J / Proteins / Urea effects on protein stability: hydrogen bonding and the hydrophobic effect. by Q Zou (1998)
  21. 10.1021/ja002064f / J Am Chem Soc / Molecular dynamics study of hydrophobic effects in aqueous urea solutions. by M Ikeguchi (2001)
  22. 10.1021/ja020496f / J Am Chem Soc / Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. by RD Mountain (2003)
  23. 10.1039/b413167c / Phys Chem Chem Phys / Methane clustering in explicit water: effect of urea on hydrophobic interactions. by C Oostenbrink (2005)
  24. 10.1021/ja058600r / J Am Chem Soc / Does urea denature hydrophobic interactions? by ME Lee (2006)
  25. 10.1021/ja069232+ / J Am Chem Soc / Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. by EP O'Brien (2007)
  26. {'key': 'ref26', 'first-page': '1', 'article-title': 'Protein denaturation. C. Theoretical models for the mechanism of denaturation.', 'volume': '24', 'author': 'C Tanford', 'year': '1970', 'journal-title': 'Adv Protein Chem'} / Adv Protein Chem / Protein denaturation. C. Theoretical models for the mechanism of denaturation. by C Tanford (1970)
  27. 10.1021/bi00107a010 / Biochemistry / Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. by SE Jackson (1991)
  28. 10.1016/0010-4655(95)00042-E / Comput Phys Comm / Gromacs: a message-passing parallel molecular dynamics implementation. by HJC Berendsen (1995)
  29. 10.1007/s008940100045 / J Mol Model / Gromacs 3.0: a package for molecular simulation and trajectory analysis. by E Lindahl (2001)
  30. 10.1002/jcc.20291 / J Comput Chem / Gromacs: fast, flexible, and free. by DVD Spoel (2005)
  31. 10.1021/ja9621760 / J Am Chem Soc / Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. by WL Jorgensen (1996)
  32. 10.1021/jp003919d / J Phys Chem B / Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. by GA Kaminski (2001)
  33. 10.1063/1.445869 / J Chem Phys / Comparison of simple potential functions for simulating liquid water. by WL Jorgensen (1983)
  34. 10.1021/jp030534x / J Phys Chem B / Computer simulation of urea-water mixtures: a test of force field parameters for use in biomolecular simulation. by LJ Smith (2004)
  35. 10.1063/1.464397 / J Chem Phys / Particle mesh ewald: an <italic>N</italic> log(<italic>N</italic>) method for ewald sums in large systems. by T Darden (1993)
  36. 10.1063/1.470117 / J Chem Phys / A smooth particle mesh ewald method. by U Essmann (1995)
  37. 10.1063/1.448118 / J Chem Phys / Molecular dynamics with a coupling to an external bath. by HJC Berendsen (1984)
  38. 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H / J Comp Chem / LINCS: a linear constraint solver for molecular simulations. by B Hess (1997)
  39. 10.1093/nar/28.1.235 / Nucleic Acids Res / The protein data bank. by HM Berman (2000)
  40. 10.1073/pnas.91.1.311 / Proc Natl Acad Sci U S A / Direct observation of better hydration at the N terminus of an α-helix with glycerine rather than alanine as the N-cap residue. by Y Harpaz (1994)
  41. 10.1016/0263-7855(90)80070-V / J Mol Graph / What if: a molecular modeling and drug design program. by G Vriend (1990)
  42. 10.1021/jp066474n / J Phys Chem B / Aqueous urea solutions: structure, energetics, and urea aggregation. by MC Stumpe (2007)
  43. 10.1016/j.jmb.2005.11.058 / J Mol Biol / The solvation interface is a determining factor in peptide conformational preferences. by EJ Sorin (2006)
  44. 10.1002/jcc.540160303 / J Comput Chem / The double cubic lattice method: Efficient approaeches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. by F Eisenhaber (1995)
  45. 10.1002/bip.360221211 / Biopolymers / Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. by W Kabsch (1983)
  46. 10.1021/ja076216j / J Am Chem Soc / Interaction of urea with amino acids: implications for urea-induced protein denaturation. by MC Stumpe (2007)
  47. 10.1021/bi00093a002 / Biochemistry / Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis. by SE Jackson (1993)
  48. 10.1063/1.2185105 / J Chem Phys / Osmotic coefficients of atomistic NaCl (aq) force fields. by B Hess (2006)
  49. 10.1006/jmbi.1995.0616 / J Mol Biol / The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. by LS Itzhaki (1995)
  50. 10.1006/jmbi.1997.1612 / J Mol Biol / The changing nature of the protein folding transition state: implications for the shape of the free-energy profile for folding. by M Oliveberg (1998)
  51. 10.1073/pnas.91.22.10422 / Proc Natl Acad Sci U S A / Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. by D Otzen (1994)
  52. 10.1098/rstb.1995.0040 / Philos Trans R Soc Lond B Biol Sci / Mapping the structures of transition states and intermediates in folding: delineation of pathways at high resolution. by AR Fersht (1995)
  53. 10.1006/jmbi.1996.0647 / J Mol Biol / Titration properties and thermodynamics of the transition state for folding: comparison of two-state and multi-state folding pathways. by YJ Tan (1996)
  54. 10.1073/pnas.241378398 / Proc Natl Acad Sci U S A / Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. by L Li (2001)
  55. 10.1002/bip.1968.360060911 / Biopolymers / New chain conformations of poly(glutamic acid) and polylysine. by ML Tiffany (1968)
  56. 10.1110/ps.0217402 / Protein Sci / A simple model for polyproline II structure in unfolded states of alanine-based peptides. by RV Pappu (2002)
  57. 10.1021/bi050124u / Biochemistry / Urea promotes polyproline II helix formation: implications for protein denatured states. by SJ Whittington (2005)
  58. 10.1073/pnas.0409693102 / Proc Natl Acad Sci U S A / Unusual compactness of a polyproline type II structure. by B Zagrovic (2005)
  59. 10.1073/pnas.0510549103 / Proc Natl Acad Sci U S A / Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. by J Makowska (2006)
  60. 10.1021/bi0474822 / Biochemistry / Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. by AK Jha (2005)
  61. 10.1021/ja075034m / J Am Chem Soc / Urea orientation on protein surfaces. by X Chen (2007)
  62. 10.1016/j.sbi.2007.12.013 / Curr Opin Struct Biol / Rattling the cage: computational models of chaperonin-mediated protein folding. by J England (2008)
  63. 10.1038/41944 / Nature / The crystal structure of the asymmetric GroEL-GroES-(ADP)<sub>7</sub> chaperonin complex. by Z Xu (1997)
  64. 10.1529/biophysj.103.037333 / Biophys J / The unfolding action of groel on a protein substrate. by A van der Vaart (2004)
  65. 10.1073/pnas.94.3.826 / Proc Natl Acad Sci U S A / The folding pathway of a protein at high resolution from microseconds to seconds. by B Nölting (1997)
  66. 10.1073/pnas.92.24.10869 / Proc Natl Acad Sci U S A / Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. by AR Fersht (1995)
Dates
Type When
Created 16 years, 9 months ago (Nov. 13, 2008, 5:38 p.m.)
Deposited 3 years, 11 months ago (Sept. 20, 2021, 6:16 p.m.)
Indexed 1 month, 1 week ago (July 28, 2025, 2:39 a.m.)
Issued 16 years, 9 months ago (Nov. 14, 2008)
Published 16 years, 9 months ago (Nov. 14, 2008)
Published Online 16 years, 9 months ago (Nov. 14, 2008)
Funders 0

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@article{Stumpe_2008, title={Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation}, volume={4}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.1000221}, DOI={10.1371/journal.pcbi.1000221}, number={11}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Stumpe, Martin C. and Grubmüller, Helmut}, editor={Pande, Vijay S.}, year={2008}, month=nov, pages={e1000221} }