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.

 

About Danilo Roccatano

I have a Doctorate in chemistry at the University of Roma “La Sapienza”. I led educational and research activities at different universities in Italy, The Netherlands, Germany and now in the UK. I am fascinated by the study of nature with theoretical models and computational. For years, my scientific research is focused on the study of molecular systems of biological interest using the technique of Molecular Dynamics simulation. I have developed a server (the link is in one of my post) for statistical analysis at the amino acid level of the effect of random mutations induced by random mutagenesis methods. I am also very active in the didactic activity in physical chemistry, computational chemistry, and molecular modeling. I have several other interests and hobbies as video/photography, robotics, computer vision, electronics, programming, microscopy, entomology, recreational mathematics and computational linguistics.
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