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:
- 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.
- 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
LIST OF SOLVENTS
LIST OF FORCE FIELDS
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 | ||
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GIGAVLKVLTTGLPALISWIKRKRQQNH2 |
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| 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 | ||
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RGWSVQNGKYTNNGKTTEGR |
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| 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  -HAIRPIN from Protein G B1 domain: Protein G is an immunoglobulin-binding protein expressed in group C and G Streptococcal bacteria. BACK |
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GEWTYDDATKTFTVTE |
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| 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: Alamethicin (PDB-code:1AML): |
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Ac-Aib-P-Aib-A-Aib-A-Q-Aib-V-Aib-G-L-Aib-P-V-Aib-Aib-Q-Q-Phl |
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| 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 |
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| AIB-RICH PEPTIDE II: It is a synthetic peptide containing 7 Aib and 1 Leu amino acids. BACK | ||
|
(Aib)5-Leu-(Aib)2 |
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| 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] |
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| 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 |
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| 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 |
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| 1: β3-octapeptide.
2: tethered 3,4: Mixed peptide (α/β) |
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| 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) |
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| 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 |
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| 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 |
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| 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 |
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| 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 | ||
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Ac-KTNMKHMAGAAAAGAVVGGLG-NH2 |
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| 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  -helical form the isoform PrPSc. BACK |
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DWEDRYYREN |
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| 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 |
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| 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 | ||||||
| A1-42 |
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DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA |
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| 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 |
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KLVFFAE |
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| 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 A16-22 Ace-KLVFFAE-NH2 |
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| 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 | ||||||
| A40 |
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| 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 | ||||||
| A25-35 |
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GSNKGAIIGLM |
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| 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 | ||
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AETAAAKFLREHMDS |
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| 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 | ||
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LGLLLRHLRHHSNLLANI |
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| 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 receptors. BACK | ||
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DRVYVHPF |
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| 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 |
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| 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 peptide. BACK | ||
|
Ac-AA(AAKAA)3AAY-NMe |
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| (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 samariensis. BACK | ||
|
GLLKRIKTLL |
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| 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 |
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| 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 |
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| 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 Uperoleia. BACK | ||
| Aurein 1.2 | ||
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GLFDIIKKIAESF-NH2 |
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| Maculatin 1.1 | ||
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GLFGVLAKVAAHVVPAIAEHF-NH2 |
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| Citropin 1.1 | ||
| GLFDVIKKVASVIGGL-NH2 | ||
| Caerin 1.1 | ||
|
GLLSVLGSVAKHVLPHVVPVIAEHL-NH2 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 | ||
daniloroccatano.blog 
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.
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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.
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