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

SIMPEOS_LOGO
SIMPEOS is a simple hypertextual database that provides a list of peptides 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!



PEPTIDES                     SOLVENTS           FORCE-FIELDS


LIST OF PEPTIDES

Melittin
Betanova
Alamethicin
41-56 \beta-hairpin from Protein G B1 domain
Aib-rich peptide II
Leu/Met-enkephalins
\beta-peptides
Fluorinated \beta-peptides
E7
Galanin
Designed Peptide
Bombesin
Channel forming peptide
Myoglobin C-term
Prion Protein peptides
Prion H1 peptide
Amyloid- \beta-peptid e
Blocked valine peptide
Derivative of C-peptide
S-peptide analogue
Fibrillogenic Binding B18
[Val5]-Angiotensin II
BBA5 Peptide
Peptide hlF1-11
AK peptide
Anoplin
Peptide sMTM7
A\beta (1-42) peptide
Magainin 2
Aureins
\beta-hairpin CLN025
Trp-Cage
Poly-glycines
Glycine-Serine
Peptide 1
TRPZIP4

LIST OF SOLVENTS

BACK


LIST OF FORCE FIELDS

BACK




DATABASE

Selection of peptides studied in different organic solvent and mixtures. The force field used for the simulation and the longest MD simulation time reported in the reference(s) are indicated.

DESCRIPTION OF THE ENTRY FIELDS 

NAME AND DESCRIPTION OF THE PEPTIDE
SEQUENCE
SOLVENT MAX SIMULATION LENGHT FORCE FIELD
BIBLIOGRAPHY

ENTRIES



MELITTIN: Antimicrobial, a Hemolytic polypeptide from Honeybee (Apis Mellifera) venom. BACK
MelittinnoFrameFluorinatedSolvents

GIGAVLKVLTTGLPALISWIKRKRQQNH2

MeOH 60 ns GROMOS
Glattli, A.; Chandrasekhar, I.; van Gunsteren, W. F., A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer. Eur. Biophys. J. Biophy. 2006, 35 (3), 255-267. Link
30 %HFIP/water 100 ns GROMOS
Roccatano, D.; Fioroni, M.; Zacharias, M.; Colombo, G., Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study. Protein Sci. 2005, 14 (10), 2582-2589. Link
30%TFE/water 30 ns GROMOS
Roccatano, D.; Colombo, G.; Fioroni, M.; Mark, A. E., Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci USA 2002, 99 (19), 12179-12184. Link
GmdCl 3 M 8 ns CHARMM
Tetrapropylammonium Sulphate 0.1 M, GmdCl 3 M 10 ns AMBER99
Mason, P. E.; Brady, J. W.; Neilson, G. W.; Dempsey, C. E., The interaction of guanidinium ions with a model peptide. Biophys.J. 2007, 93 (1), L4-L6. Link

BETANOVA: Designed peptide in the group of Prof L. Serrano to adopt a three-strand conformation in solution. BACK
 BetanovaBetanovaTFE

RGWSVQNGKYTNNGKTTEGR

30%TFE/water 20 ns GROMOS
Roccatano, D.; Colombo, G.; Fioroni, M.; Mark, A. E., Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci USA 2002, 99 (19), 12179-12184. Link

41-56 \beta-HAIRPIN from Protein G B1 domain: Protein G is an immunoglobulin-binding protein expressed in group C and G Streptococcal bacteria. BACK
Beta-hairpinbeta-haipinTFE.png

GEWTYDDATKTFTVTE

30%TFE/water 30 ns GROMOS
Roccatano, D.; Colombo, G.; Fioroni, M.; Mark, A. E., Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci USA 2002, 99 (19), 12179-12184. Link
Trehalose 0-0.26 M 20 ns GROMOS
Sessions, R. B.; Gibbs, N.; Dempsey, C. E., Hydrogen Bonding in Helical Polypeptides from Molecular Dynamics Simulations and Amide Hydrogen Exchange Analysis: Alamethicin and Melittin in Methanol. Biophys. J. 1998, 74, 138-152. Link

ALAMETHICIN: a channel-forming peptide antibiotic, produced by the fungus Trichoderma viride. It belongs to peptaibol peptides which contain the non-proteinogenic amino acid residue Aib (2-Aminoisobutyric acid). BACK
Aib:
Alpha-aminobutyric_acidAlamethicin (PDB-code:1AML):Alam

Ac-Aib-P-Aib-A-Aib-A-Q-Aib-V-Aib-G-L-Aib-P-V-Aib-Aib-Q-Q-Phl

MeOH 1 ns GROMOS and CVFF
Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E., Peptide folding: When simulation meets experiment. Angew. Chem. Int. Ed. 1999, 38 (1-2), 236-240. Link

van der Spoel, D.; Berendsen, H. J. C., Molecular dynamics simulation of Leu-Enkephalin in water and DMSO. Bioph. J. 1997, 72, 2032-2041. Link

Daura, X.; Gademann, K.; Schäffer, H.; Jaun, B.; Seebach, D.; van Gunsteren, W. F., The a-Peptide Hairpin in Solution: Conformational Study of a beta-Hexapeptide in Methanol by NMR Spectroscopy and MD Simulation. J. Am. Chem Soc. 2001, 123, 2393-2404. Link


AIB-RICH PEPTIDE II: It is a synthetic peptide containing 7 Aib and 1 Leu amino acids. BACK

(Aib)5-Leu-(Aib)2

MeOH 0.15 ns GROMOS
Zagrovic, B.; Gattin, Z.; Lau, J. K.-C.; Huber, M.; van Gunsteren, W. F., Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment. Eur. Bioph. J. with Biophys. Lett. 2008, 37 (6), 903-912. Link

LEU/MET-ENKEPHALINS: They are naturally occurring endogenous opioid peptides that have opioid effects of a relatively short duration. The enkephalins are considered to be the primary endogenous ligands of the δ-opioid receptor, due to their high potency and selectivity for the site over the other endogenous opioids. BACK

Y-G-G-F-[L/M]

MeOH 2 ns GROMOS
Daura, X.; Antes, I.; van Gunsteren, W. F.; Theil, W.; Mark, A. E., The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Struct. Funct. and Genet. 1999, 36, 542-555. Link

β-peptides: β-peptides consist of β amino acids, which have their amino group bonded to the β carbon rather than the α carbon as in the 20 standard biological amino acids. The only common naturally occurring β amino acid is β-alanine; although it is used as a component of larger bioactive molecules, β-peptides, in general, do not appear in nature. For this reason, β-peptide-based antibiotics are being explored as ways of evading antibiotic resistance. BACK
β-hexapeptides
H(β2-hVal)(β3-hAla)(β2-hLeu)(β3-hVal)(β2-hAla)(β3-hLeu)-OH

H(β3-hVal)(β3-hAla)(β3-hLeu)((S,S)-β3-hAla(aMe)) (β3-hVal)(β3-hAla)-(β3-hLeu)-OH

MeOH 50-100 ns GROMOS
Zagrovic, B.; Gattin, Z.; Lau, J. K.-C.; Huber, M.; van Gunsteren, W. F., Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment. Eur. Bioph. J. with Biophys. Lett. 2008, 37 (6), 903-912. Link

Daura, X.; Antes, I.; van Gunsteren, W. F.; Theil, W.; Mark, A. E., The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Struct. Funct. and Genet. 1999, 36, 542-555. Link

Daura, X.; van Gunsteren, W. F.; Mark, A. E., Folding-unfolding thermodynamics of a beta-heptapeptide. Proteins: Struct. Funct. and Genet. 1999, 34, 269-280. Link

Reif, M. M.; Kraeutler, V.; Kastenholz, M. A.; Daura, X.; Huenenberger, P. H., Molecular Dynamics Simulations of a Reversibly Folding beta-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions. J. Phys. Chem. B 2009, 113 (10), 3112-3128. Link

Niggli, D. A.; Ebert, M.-O.; Lin, Z.; Seebach, D.; van Gunsteren, W. F., Helical Content of a beta(3)-Octapeptide in Methanol: Molecular Dynamics Simulations Explain a Seeming Discrepancy between Conclusions Derived from CD and NMR Data. Chem. Eur. J. 2012, 18 (2), 586-593. Link

Wang, D.; Jaun, B.; van Gunsteren, W. F., Folding, and Unfolding of Two Mixed alpha/beta Peptides. ChemBioChem 2009, 10 (12), 2032-2041. Link

1: β3-octapeptide.

2: tethered

3,4: Mixed peptide (α/β)

1: (β3‐V)(β3‐K)(β3‐R)BSP(β3‐F)(β3‐E)(β3‐R)BSP(β3‐Y)(β3‐I)‐OH

2: (β3‐V)(β3‐K)(β3‐R)BSE(β3‐F)(β3‐E)(β3‐R)BSE(β3‐Y)(β3‐I)‐OH

3: (β2-(S)-F)H(β2-(S)-L)(β3-(R)-V)I(β3-(S)-Y)

4: Aib(β3-(S)-Y)Aib(β3-(S)-K)Aib(β3-(S)-D)Aib(β3-(R)-V)

MeOH 100-200 ns GROMOS
Wang, D.; Jaun, B.; van Gunsteren, W. F., Folding and Unfolding of Two Mixed alpha/beta-Peptides. ChemBioChem 2009, 10 (12), 2032-2041. Link
Fluorinated β-peptides. BACK
 
1: H-(β-hVal)(β-hAla)(β-hLeu)((S,S)-β-H)Ala(α-F)(β-hVal)(β-hAla)(β-hLeu)-OH

2: H(β-hVal)(β-hAla)(β-hLeu)((S,R)-β-hAla(α-F))(β-hVal)(β-hAla)(β-hLeu)-OH

3: H(β-hVal)(β-hAla)(β-hLeu)-((S)-β-hAla(di-α-F))(β-hVal)(β-hAla)(β-hLeu)-OH

MeOH 100 ns GROMOS
Gattin, Z.; van Gunsteren, W. F., Influence of Backbone Fluorine Substitution upon the Folding Equilibrium of a beta-Heptapeptide. J. Phys. Chem. B 2009, 113 (25), 8695-8703. Link

GALANIN: it is a neuropeptide encoded by the GAL gene, that is widely expressed in the brain, spinal cord, and gut of humans as well as other mammals. BACK
GWTLNSAGYLLGPHAIDNHRSFSDKHGLT-NH2
TFE 0.12 ns CHARMM
De Loof, H.; Nilsson, L.; Rigler, R., Molecular Dynamics Simulation of Galanin in aqueous and non-aqueous solution. J. Am. Chem. Soc. 1992, 114, 4028-4035. Link

E7. BACK
 
EPAEAAK
ETH/TFE/HFIP 0.02 ns CVFF
Dwyer, D. S., Molecular simulation of the effects of alcohols on peptide structure. Biopolymers 1999, 49 (7), 635-645. Link

A design peptide. BACK
Ac-DTESILRZAFELHNK-NH2
50% TFE/water 0.5 ns AMBER
Bodkin, M. J.; Goodfellow, J. M., Hydrophobic Solvation in Aqueous Trifluoroethanol Solution. Biopolymers 1996, 39, 43-50. Link

BOMBESIN: it is a 14-amino acid peptide originally isolated from the skin of the European fire-bellied toad.  It stimulates gastrin release from G cells. BACK
ZRLGNZWAVGHLM-NH2
30% TFE/water 10 ns GROMOS
Diaz, M. D.; Fioroni, M.; Burger, K.; Berger, S., Evidence of complete hydrophobic coating of bombesin by trifluoroethanol in aqueous solution: an NMR spectroscopic and molecular dynamics study. Chem. Eur. J. 2002, 8, 1663-1669. Link

CHANNEL FORMING PEPTIDE. BACK

KKKKPARVGLGITTVLTMTTQS

30% TFE/water 20 ns GROMOS
Johnston, J. M.; Cook, G. A.; Tomich, J. M.; Sansom, M. S. P., Conformation and environment of channel-forming peptides: a simulation study. Bioph. J. 2006, 90, 1855-1864. Link

Myoglobin C-terminal region. BACK

NKALNLFRKDIAAKYKELGYNG

30% TFE/water 0.2 ns GROMOS
van Buuren, A. R.; Berendsen, H. J. C., Molecular Dynamics Simulation of the stability of a 22-residue α-Helix in water and 30% trifluoroethanol. Biopolymers 1993, 33, 1159-1166. Link

PrP106-126: it is a fragment of the Prion Protein (PrP). This is a protein expressed most predominant in the nervous system (but occurs in many other tissues throughout the body) in mammals that can exist in multiple isoforms. The misfolded version (called scrapie or PrPSc) is associated with a variety of cognitive disorders and neurodegenerative diseases. BACK

Ac-KTNMKHMAGAAAAGAVVGGLG-NH2

TFE, Hexane, DMSO 100 ns GROMOS
Daidone, I.; Simona, F.; Roccatano, D.; Broglia, R. A.; Tiana, G.; Colombo, G.; Di Nola, A., Proteins: Struct. Funct. and Bioinformatics 2004, 57, 198.  Link

H1 helix from the mouse PrP: This is another fragment of the PrP corresponding to the region that assumes \alpha-helical form the isoform PrPSc. BACK

DWEDRYYREN

Urea 3.94M GdmCl 3.05 M 35 ns CHARMM22
O’Brien, E. P.; Dima, R. I.; Brooks, B.; Thirumalai, D., Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism. J. Am. Chem. Soc. 2007, 129 (23), 7346-7353. Link

Derivatives of the C-peptide (or the connecting peptide) that is a short 31-amino-acid polypeptide that connects insulin’s A-chain to its B-chain in the proinsulin molecule. BACK

1) Suc- AETAAAKFLRNHA-NH2

2) Suc- AKERAFTANAHLA-NH2

Urea 8M 10 ns CHARMM
Caballero-Herrera, A.; Nordstrand, K.; Berndt, K. D.; Nilsson, L., Effect of urea on peptide conformation in water: Molecular dynamics and experimental characterization. Bioph. J. 2005, 89 (2), 842-857.  Link

Amyloid beta (Aβ or Abeta) denotes peptides that are crucially involved in Alzheimer’s disease as the main component of the amyloid plaques found in the brains of Alzheimer patients. BACK
A\beta1-42

DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA

HFIP, TFE, DMSO 20 ns GROMOS
Yang, C.; Li, J.; Li, Y.; Zhu, X., The effect of solvents on the conformations of Amyloid beta-peptide (1-42) studied by molecular dynamics simulation. J. Mol. Struct.-Theochem 2009, 895 (1-3), 1-8. Link

A\beta16-22 Fragment

KLVFFAE

Urea 8M 10 ns AMBER/OPLS
Klimov, D. K.; Straub, J. E.; Thirumalai, D., Aqueous urea solution destabilizes Ab16-22 oligomers. Proc. Natl. Acad. Sci. USA 2004, 101 (41), 14760-14765.  Link
Capped form of A\beta16-22 Ace-KLVFFAE-NH2
Trehalose (0-0.18 mol/L) 300 ns GROMOS
Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y., Molecular Insight into the Inhibition Effect of Trehalose on the Nucleation and Elongation of Amyloid beta-Peptide Oligomers. J. Phys. Chem. B 2009, 113 (32), 11320-11329. Link
A\beta40
Trehalose (0-0.18 mol/L) 300 ns GROMOS
Liu, F. F.; Ji, L.; Dong, X. Y.; Sun, Y., Molecular Insight into the Inhibition Effect of Trehalose on the Nucleation and Elongation of Amyloid beta-Peptide Oligomers. J. Phys. Chem. B 2009, 113 (32), 11320-11329. Link
A\beta25-35

GSNKGAIIGLM

Wei, G.; Shea, J.-E., Effects of Solvent on the Structure of the Alzheimer Amyloid-ß(25–35) Peptide. Biophys. J. 2006, (91), 1638-1647.  Link

 S-peptide analog: it is the analog of the S-peptide an enzymatically inactive product of the limited digestion of ribonuclease A by subtilisin. BACK

AETAAAKFLREHMDS

Urea 8M 20 ns GROMOS
Zhang, Z.; Zhu, Y.; Shi, Y., Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue. Biophys. Chem. 2001, 89, 145-162.  Link 

Fibrillogenic Binding B18: it a peptide from the sea urchin sperm binding protein. BACK

LGLLLRHLRHHSNLLANI

30 % TFE/water 50 ns GROMOS
Knecht, V.; Mohwald, H.; Lipowsky, R., Conformational diversity of the fibrillogenic fusion peptide B18 in different environments from molecular dynamics simulations. J. Phys. Chem. B 2007, 111 (16), 4161-4170. Link

[Val5]-ANGIOTENSIN II: Angiotensin II analog that is an agonist AT1 angiotensin receptorsBACK

DRVYVHPF

25% Methanol/ water 300 ns AMBER
Gerig, J. T., Investigation of Methanol-Peptide Nuclear Overhauser Effects through Molecular Dynamics Simulations. J. of Phys. Chem. B 2012, 116 (6), 1965-1973. Link

BBA5 Peptide: a designed peptide with beta-beta-alpha structure. BACK
YRVDPSYDFSRSDELAKLLRQHAG
50% Methanol/ water 224 ns AMBER
Hwang, S.; Shao, Q.; Williams, H.; Hilty, C.; Gao, Y. Q., Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins – A Combined Molecular Dynamics and NMR study. J. Phys. Chem. B 2011, 115 (20), 6653-6660. Link
Various 30-40% (v/v) water Mixture of TFE, MeOH, Glycerol 170 ns AMBER
Shao, Q.; Fan, Y.; Yang, L.; Gao, Y. Q., From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J. Chem. Phys. 2012, 136 (11). Link

PEPTIDE hlF1-11: Synthetic antimicrobial peptide. BACK

GRRRSVQWCA

Pure methanol, 4:4:1 methanol–chloroform–water 100 ns AMBER
Fornili, S. L.; Pizzi, R.; Rebeccani, D., Conformational Analysis of a Synthetic Antimicrobial Peptide in Water and Membrane-Mimicking Solvents: A Molecular Dynamics Simulation Study. Intr. J. Pept. Res. and Ther. 2010, 16 (4), 223-231. Link

AK PEPTIDE: model peptideBACK

Ac-AA(AAKAA)3AAY-NMe

(0-100)% methanol/water 40 ns AMBER
Paschek, D.; Puehse, M.; Perez-Goicochea, A.; Gnanakaran, S.; Garcia, A. E.; Winter, R.; Geiger, A., The Solvent-Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface. ChemPhysChem 2008, 9 (18), 2742-2750. Link

ANOPLIN: antimicrobial peptide from the venom of the solitary wasp Anoplius samariensisBACK

GLLKRIKTLL

30% TFE/water 8 ns GROMOS
Dos Santos Cabrera, M. P.; Arcisio-Mirandaa, M.; Broggio Costa, S. T.; Konno, K.; Ruggiero, J. R.; Procopio, J.; Neto, J. R., Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus. J. Pep. Sci. 2008, 14 (6), 661-669. Link

PEPTIDE sMTM7: designed α-Helical transmembrane peptide. BACK

EFCLNCVSHTASYLRLWALSLAHAQ

DMSO 10 ns GROMOS
Duarte, A. M. S.; van Mierlo, C. P. M.; Hemminga, M. A., Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO. J. of Phys. Chem. B 2008, 112 (29), 8664-8671. Link

Magainin 2: it is one of the magainins, a class of antimicrobial peptides found in the African clawed frog (Xenopus laevis). BACK

GIGKFLHSAKKFGKAFVGEIMNS

Various water mixtures of Urea, GmdCl, TFE 40 ns GROMOS
Mehrnejad, F.; Khadem-Maaref, M.; Ghahremanpour, M. M.; Doustdar, F., Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study. J. Comp.-Aid. Mol. Des. 2010, 24 (10), 829-841. Link
TFE/H2O(10M),Sorbitol/H2O(0.5M),Glycerol/H2O(4M) 100 ns GROMOS
Mehrnejad, F.; Ghahremanpour, M. M.; Khadem-Maaref, M.; Doustdar, F., Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation. J. Chem. Phys. 2011, 134 (3). Link 

Aureins: it is a family of antibacterial peptides. They are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus UperoleiaBACK
Aurein 1.2

GLFDIIKKIAESF-NH2

Maculatin 1.1

GLFGVLAKVAAHVVPAIAEHF-NH2

Citropin 1.1
GLFDVIKKVASVIGGL-NH2
Caerin 1.1

GLLSVLGSVAKHVLPHVVPVIAEHL-NH2

50 % TFE/water 200 ns GROMOS 54A7
Chen, R.; Mark, A. E., The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action. Eur. Biophys. J. with Biophys. Lett. 2011, 40 (4), 545-553. Link

CLN025: it is a miniprotein variant of chignolin. BACK

YYDPETGTWY

TFE, MeOH, and DMSO 200 ns GROMOS (53A6)
Hatfield, M. P. D.; Murphy, R. F.; Lovas, S., Molecular Dynamics Analysis of the Conformations of beta-Hairpin Miniprotein. J. Phys. Chem. B 2010, 114 (8), 3028-3037. Link
GmdCl 3,6 M, Urea 4,8 M 200 ns GROMOS (53A6)
Hatfield, M. P. D.; Murphy, R. F.; Lovas, S., The CLN025 Decapeptide Retains a beta-Hairpin Conformation in Urea and Guanidinium Chloride. J. Phys. Chem. B 2011, 115 (17), 4971-4981. Link

Trp-Cage: it is a synthetic 20-residue mini protein which folds rapidly and spontaneously to a well-defined globular structure more typical of larger proteins. BACK

NLYIQWLKDGGPSSGRPPPS

Urea 1.9-5.8 M 32500 a) Amber
Canchi, D. R.; Paschek, D.; Garcia, A. E., Equilibrium Study of Protein Denaturation by Urea. J. Am. Chem. Soc. 2010, 132 (7), 2338-2344. Link
GmdCl 2M, Urea 2 M 1000 Amber (ff99)
Heyda, J.; Kozisek, M.; Bednarova, L.; Thompson, G.; Konvalinka, J.; Vondrasek, J.; Jungwirth, P., Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein. J. Phys. Chem. B 2011, 115 (28), 8910-8924. Link

Poly-glycines peptides. BACK

G2–5

Urea 2M, TMAO 2M 2 ns CHARMM-27
Hu, C. Y.; Kokubo, H.; Lynch, G. C.; Bolen, D. W.; Pettitt, B. M., Backbone additivity in the transfer model of protein solvation. Protein Sci. 2010, 19 (5), 1011-1022.  Link

GGG

Glycine betaine, Urea 300 ns CHARMM27
Ma, L.; Pegram, L.; Record, M. T.; Cui, Q., Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry 2010, 49 (9), 1954-1962. Link

G15

Urea 8M 50 ns OPLS-AA/L
Tran, H. T.; Mao, A.; Pappu, R. V., Role of backbone – Solvent interactions in determining conformational equilibria of intrinsically disordered proteins. J. Am. Chem. Soc. 2008, 130 (23), 7380-7392. Link

Glycine-serine peptides. BACK

(GS)8

Urea 2M, TMAO 2M 2 ns CHARMM-27
Tran, H. T.; Mao, A.; Pappu, R. V., Role of backbone – Solvent interactions in determining conformational equilibria of intrinsically disordered proteins. J. Am. Chem. Soc. 2008, 130 (23), 7380-7392. Link

Peptide 1: a fast folding peptides synthetic peptide. BACK

SESYINPDGTWTVTE

Urea 5 M 200 AMBER99
Wei, H. Y.; Shao, Q. A.; Gao, Y. Q., The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins. Phys. Chem. Chem. Phys. 2010, 12 (32), 9292-9299. Link

TRPZIP4: tryptophan zippers, a stable, monomeric β-hairpin. BACK

GEWTWDDATKTWTWTE

Urea 5M 200 AMBER99
Wei, H. Y.; Shao, Q. A.; Gao, Y. Q., The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins. Phys. Chem. Chem. Phys. 2010, 12 (32), 9292-9299. Link

 

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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2 Responses to COMPUTER SIMULATIONS STUDIES OF PEPTIDES IN ORGANIC SOLVENTS AND COSOLVENTS: A SIMPLE DATABASE

  1. Alex says:

    I am no longer positive the place you’re getting your info, however great topic. I must spend a while studying much more or figuring out more. Thank you for magnificent info I was looking for this info for my mission.

    Like

    • Thank you very much for your comment. I fully agree that it is the time to update this list with the development in the field in the last 6 years but I am glad to read that these information are still useful. Soon a not-yet-updated (sorry!) list for the proteins based on the same book chapter will be also published.

      Like

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