COMPUTER SIMULATIONS STUDIES OF PROTEINS IN ORGANIC SOLVENTS AND COSOLVENTS: A SIMPLE DATABASE

SIMPROS_LOGO

SIMPROS is a simple hypertextual database that provides a list of proteins that have been studied using molecular dynamics simulations in non-aqueous solvents. The current version is based on my previous two reviews:

  1. D. Roccatano. Computer simulations study of biomolecules in non-aqueous solutions.  In Advances in Protein and Peptide Sciences. (2013), Vol. 1, Ed. Ben M. Dunn. Bentham Science Publisher. Preprint here.
  2. Roccatano. Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions Current Peptide and Peptide Science. 9(4), 407-426, (2008).
This initial version covers the period 1995-2012.

Suggestions to improve, correct and keep update this list are welcome!

NOTE THE SITE IS UNDER CONSTRUCTION



PROTEINS                     SOLVENTS           FORCE-FIELDS



LIST OF PROTEINS

Ubiquitin
Cutinase
Pseudolysin
Thermolysin
Barnase
CI2
Cytochrome C
Monooxygenase P450 BM3
Subtilisin BPN’
Subtilisin Carlsberg
Acylphospatase
Myoglobin
Lysozime
α-Chymotrypsin
Lipase B
Burkholderia cepacia lipase
β-2 microglobulin
Protein L
Villin headpiece protein
Human zinger Finger Protein
Triosephosphate isomerase from Trypanosoma cruzi
Cardosin A
Cold Shock protein Bc-CsP from Bacillus caldolyticus

DATABASE

Ubiquitin

Hexane

5

GROMOS
Pieraccini, S.; Sironi, M.; Colombo, G., Modeling enzymatic processes: a molecular simulation analysis of the origins of regioselectivity. Chem. Phys. Lett. 2006, 418, 373-376.
Zhu, L. J.; Yang, W.; Meng, Y. Y.; Xiao, X. C.; Guo, Y. Z.; Pu, X. M.; Li, M. L., Effects of Organic Solvent and Crystal Water on gamma- Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation. J. Phys. Chem. B 2012, 116 (10), 3292-3304.

60% MeOH/water

0.5

ENCAD [282]
Alonso, D. O. V. and Daggett, V.; (1995) Bioph. J. 2006, 90, 1855-1864.
Cutinase

Pure diisopropyl ether and water mixtures

10

GROMOS
Allison, J. R.; Mueller, M.; van Gunsteren, W. F., A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability. Protein Sci. 2010, 19 (11), 2186-2195.
Allison, J. R.; Mueller, M.; van Gunsteren, W. F., A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability. Protein Sci. 2010, 19 (11), 2186-2195.

Pure EtOH and water mixtures

10

GROMOS
Allison, J. R.; Mueller, M.; van Gunsteren, W. F., A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability. Protein Sci. 2010, 19 (11), 2186-2195.

Allison, J. R.; Mueller, M.; van Gunsteren, W. F., A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability. Protein Sci. 2010, 19 (11), 2186-2195.

Pure Hexane and water mixtures

4/10

GROMOS
Pieraccini, S.; Sironi, M.; Colombo, G., Modeling enzymatic processes: a molecular simulation analysis of the origins of regioselectivity. Chem. Phys. Lett. 2006, 418, 373-376.
Zhu, L. J.; Yang, W.; Meng, Y. Y.; Xiao, X. C.; Guo, Y. Z.; Pu, X. M.; Li, M. L., Effects of Organic Solvent and Crystal Water on gamma- Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation. J. Phys. Chem. B 2012, 116 (10), 3292-3304.

Pure Hexane and water mixtures

4/10

GROMOS

Allison, J. R.; Mueller, M.; van Gunsteren, W. F., A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability. Protein Sci. 2010, 19 (11), 2186-2195.

Pure [BMIM][PF6] and [BMIM][NO3]

10

GROMOS96 (43A1)
Street, T. O.; Bolen, D. W.; Rose, G. D., A molecular mechanism for osmolyte-induced protein stability. Proc. Natl. Acad. Sci. USA 2006,
Pseudolysin

25 % water/EtOH

1000

GROMOS 53A6

Lousa, D.; Baptista, A. M.; Soares, C. M., Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 2012,52(2), 465-473.

Thermolysin

25 % water/EtOH

1000

GROMOS 53A6
Lousa, D.; Baptista, A. M.; Soares, C. M., Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 2012,52(2), 465-473.
Barnase

Urea 8 M

0.8/2

CHARMM and OPLS
  • Tirado-Rives, J.; Orozco, M.; Jorgensen, W. L., Molecular Dynamics Simulations of the Unfolding of Barnase in Water and 8 M Aqueous Urea. Biochemistry 1997,36, 7313-7329.
  • Calflish, A.; Karplus, M., Structural details of urea binding to barnase: a molecular dynamics analysis. Structure 1999,7, 477.
CI2

Hexane

0.3

AMBER

Toba, S.; Hartsough, D. S.; Merz, K. M., Solvation and dynamics of chymotrypsin in hexane. J. Am. Chem. Soc. 1996,118(27), 6490-6498.


Urea 8 M

20

ENCAD

Bennion, B. J.; Daggett, V., The molecular basis for the chemical denaturation of proteins by urea. Proc. Natl Acad. Sci.  USA 2003,100(9), 5142-5147.


Urea 4 M

10

ENCAD
Bennion, B. J.; Daggett, V., Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: A chemical chaperone at atomic resolution. Proc. Natl. Acad. Sci. USA 2004,101, 6433.

4 M TMAO/ 8 M Urea

10

ENCAD
Bennion, B. J.; Daggett, V., Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: A chemical chaperone at atomic resolution. Proc. Natl. Acad. Sci. USA 2004,101, 6433.

10 M Urea

150-800

GROMOS G53a6

Lindgren, M.; Westlund, P. O., The effect of urea on the kinetics of local unfolding processes in chymotrypsin inhibitor 2. Biophys. Chem. 2010,151(1-2), 46-53.


8 M Urea/1M Trehalose

100

GROMOS 43a1

Zhang, N.; Liu, F. F.; Dong, X. Y.; Sun, Y., Molecular Insight into the Counteraction of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation. J. Phys. Chem. B 2012,116(24), 7040-7047.


Cytochrome P450 BM3

14% (v/v) DMSO/water

15

GROMOS
  • Roccatano, D.; Wong, T. S.; Schwaneberg, U.; Zacharias, M., Structural and dynamic properties of cytochrome P450BM-3 in pure water and in a dimethylsulfoxide/water mixture. Biopolymers 2005,78(5), 259-267.
  • Roccatano, D.; Wong, T. S.; Schwaneberg, U.; Zacharias, M., Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study. Biopolymers 2006,83, 467-476.

cytochrome c

60% (v/v) Glycerol/ water

1

CHARMM

Scharnagl, C.; Reif, M.; Friedrich, J., Local compressibilities of proteins: comparison of optical experiments and simulations for horse heart cytochrome-c. Bioph. J. 2005,89, 64-75.


Subtilisin BPN

Octane

0.45

AMBER
Yang, L.; Dordick, J. S.; Garde, S., Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophys. J. 2004,87, 812-821.

THF

0.45

AMBER
Yang, L.; Dordick, J. S.; Garde, S., Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophys. J. 2004,87, 812-821.

ACN

3.6/0.45

AMBER
  • Yang, L.; Dordick, J. S.; Garde, S., Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophys. J. 2004,87, 812-821.
  • Zheng, Y. J.; Ornstein, R. L., Molecular dynamics of subtilisin Carlsberg in aqueous and nonaqueous solutions. Biopolymers 1996,38(6), 791-799.

Subtilisin Carlsberg

DMF

0.30

AMBER

Colombo, G.; Toba, S.; Merz, K. M., Rationalization of the Enantioselectivity of Subtilisin in DMF. J. Am. Chem. Soc. 1999,121, 3486-3493.


DMSO

0.74

AMBER
Zheng, Y. J.; Ornstein, R. L., A molecular dynamics and quantum mechanics analysis of the effect of DMSO on enzyme structure and dynamics: Subtilisin. J. Am. Chem. Soc. 1996,118(17), 4175-4180.

Hexane

10

GROMOS 53A6

Lousa, D.; Baptista, A. M.; Soares, C. M., Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents. Protein Sci. 2011,20(2), 379-386.


ACN

10

GROMOS 53A6

Lousa, D.; Cianci, M.; Helliwell, J. R.; Halling, P. J.; Baptista, A. M.; Soares, C. M., Interaction of Counterions with Subtilisin in Acetonitrile: Insights from Molecular Dynamics Simulations. J. Phys. Chem. B 2012,116(20), 5838-5848.


Acylphospatase

25% (v/v) TFE/water

80

GROMOS

Flöck., D.; Daidone, I.; Di Nola, A., A molecular dynamics study of acylphosphatase in aggregation-promoting conditions: the influence of trifluoroethanol/water solvent. Biopolymers 2004,75, 491-496.


Carboxy-myoglobin

Trehalose/ water glass

0.3

CHARMM
Cottone, G.; Cordone, L.; Ciccotti, G., Molecular dynamics simulation of carboxy-mioglobin embedded in a trehalose-water matrix. Bioph. J. 2001,80, 931-937.

Glycerol glass

10

CHARMM
Curtis, J. E.; Dirama, T. E.; Carri, G. A.; Tobias, D. J., Inertial suppression of protein dynamics in a binary glycerol-trehalose glass. J. Phys.  Chem. B 2006,110(46), 22953-22956.

Lysozyme

Trehalose

2.5

GROMOS
Lins, R. D.; Pereira, C. S.; Hünenberger, H., Trehalose-protein interaction in aqueous solution. Proteins: Struct. Funct. and Bioinformatics 2004,55, 177-186.

Glycerol

2

AMBER
Dirama, T. E.; Carri, G. A.; Sokolov, A. P., Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations. J. Chem.  Phys. 2005,122(24).

Glycerol/water 5.87 M

20

CHARMM42 (c32b2)
Vagenende, V.; Yap, M. G. S.; Trout, B. L., Molecular Anatomy of Preferential Interaction Coefficients by Elucidating Protein Solvation in Mixed Solvents: Methodology and Application for Lysozyme in Aqueous Glycerol. J. Phys. Chem. B 2009,113(34), 11743-11753.

Urea 8M

1000

CHARMM
Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J., Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc. Natl. Acad. Sci. USA 2008,105(44), 16928-16933.

α-Chymotrypsin

30 % TFE/water

35

GROMOS96
Rezaei-Ghaleh, N.; Amininasab, M.; Nemat-Gorgani, M., Conformational Changes of alpha-Chymotrypsin in a Fibrillation-Promoting Condition: A Molecular Dynamics Study. Biophys. J. 2008,95(9), 4139-4147.

Different polyarginine (R,RR,RRR)

100

CHARMM27
Shukla, D.; Schneider, C. P.; Trout, B. L., Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability. J. Am. Chem. Soc. 2011,133(46), 18713-18718.

ACN

8

AMBER03

Zhu, L. J.; Yang, W.; Meng, Y. Y.; Xiao, X. C.; Guo, Y. Z.; Pu, X. M.; Li, M. L., Effects of Organic Solvent and Crystal Water on gamma-Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation. J. Phys. Chem. B 2012,116(10), 3292-3304.


Candida Antartica Lipase B

Methanol chloroform.

2.5

AMBER

Trodler, P.; Pleiss, J., Modeling structure and flexibility of Candida Antarctica lipase B in organic solvents. BMC Struct. Biol. 2008,8.


Hexane, tert-butyl ether, methanol, tert- butyl alcohol

20

CHARMM27

1996, 118, 11695-11700.

Supercritical CO2/water mixtures

20

OPLS-AA
Silveira, R. L.; Martinez, J.; Skaf, M. S.; Martinez, L., Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide. J. Phys. Chem. B 2012,116(19), 5671-5678
BMIM-PF6, BMIM-NO3, BMIM-BF4, MOEMIM-BF4BAGUA-BF4, BCGUA-BF4, MCGUA-NO3, DCGUA-NO3
5

AMBER
Klaehn, M.; Lim, G. S.; Wu, P., How ion properties determine the stability of a lipase enzyme in ionic liquids: A molecular dynamics study. Phys. Chem. Chem. Phys. 2011,13(41), 18647-18660.

Burkholderia cepacia lipase

Toluene

30

Amber99
Trodler, P.; Schmid, R. D.; Pleiss, J., Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct. Biol. 2009,9.

β-2 microglobulin

26% TFE/water

60

CHARMM
Fogolari, F.; Corazza, A.; Varini, N.; Rotter, M.; Gumral, D.; Codutti, L.; Rennella, E.; Viglino, P.; Bellotti, V.; Esposito, G., Molecular dynamics simulation of beta(2)-microglobulin in denaturing and stabilizing conditions. Proteins: Struct. Funct. and Bioinformatics 2011,79(3), 986-1001.

Protein L

Urea 10 M

30

GROMOS96 (43a1)
Rocco, A. G.; Mollica, L.; Ricchiuto, P.; Baptista, A. M.; Gianazza, E.; Eberini, I., Characterization of the protein unfolding processes induced by urea and temperature. Biophys. J. 2008,94(6), 2241-2251.

Villin headpiece protein HP-35 and A doubly norleucine-substituent mutant (Lys24Nle/Lys29Nle)

Urea 5 M

200

AMBER99
Wei, H. Y.; Yang, L. J.; Gao, Y. Q., Mutation of Charged Residues to Neutral Ones Accelerates Urea Denaturation of HP-35. J. Phys. Chem. B 2010,114(36), 11820-11826.

Human zinger Finger Protein

EMIMCF_3SO_3/H_2O mixtures 2.36-4.41 M

200

CHARMM
Haberler, M.; Schroeder, C.; Steinhauser, O., Solvation studies of a zinc finger protein in hydrated ionic liquids. Phys. Chem. Chem. Phys. 2011,13(15), 6924-6938.

Triosephosphate isomerase from Trypanosoma cruzi

Decane

40

GROMOS96 (43a2)
Diaz-Vergara, N.; Pineiro, A., Molecular dynamics study of triosephosphate isomerase from Trypanosoma cruzi in water/decane mixtures. J. Phys. Chem. B 2008,112(11), 3529-3539.

Cardosin A

10, 90 % (v/v) TFE/water

100

GROMOS 53a6

Fraga, A. S.; Esteves, A. C.; Micaelo, N.; Cruz, P. F.; Brito, R. M. M.; Nutley, M.; Cooper, A.; Barros, M. M. T.; Pires, E. M. V., Functional and conformational changes in the aspartic protease cardosin A induced by TFE. Intl. J. Biol. Macro. 2012,50(2), 323-330.


Cold Shock protein Bc-CsP from Bacillus caldolyticus

Urea 8M

453

OPLS-AA

Stumpe, M. C.; Grubmuller, H., Urea Impedes the Hydrophobic Collapse of Partially Unfolded Proteins. Biophys. J. 2009,96(9), 3744-3752.

 

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