HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Abstract Full Text (PDF) All Versions of this Article: ps.051426605v1 14/10/2582    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Roccatano, D. Articles by Colombo, G. Search for Related Content PubMed PubMed Citation Articles by Roccatano, D. Articles by Colombo, G. Social Bookmarking                   What's this?

Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study

¹ School of Engineering and Science, International University of Bremen, D-28725 Bremen, Germany
² Department of Chemistry, University of Indiana, Bloomington, Indiana 47405, USA
³ Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milano, Italy

Reprint requests to: Danilo Roccatano, School of Engineering and Science, International University of Bremen, Campus Ring 1, D-28725 Bremen, Germany; e-mail: d.roccatano{at}iu-bremen.de; fax: +49-421-200-3249.

(RECEIVED March 9, 2005; FINAL REVISION June 14, 2005; ACCEPTED July 6, 2005)

	Abstract

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
The molecular mechanism by which HFIP stabilizes the -helical structure of peptides is not well understood. In the present study, we use melittin as a model to gain insight into the details of the atomistic interactions of HFIP with the peptide. We have performed extensive comparative molecular dynamics simulations (up to 100 nsec) in the absence and in the presence of HFIP. In agreement with recent NMR experiments, the simulations show rapid loss of tertiary structure in water at pH 2 but much higher helicity in 35% HFIP. The MD simulations also indicate that melittin adopts a highly dynamic global structure in 35% HFIP solution with two -helical segments sampling a wide range of angular orientations. The analysis of the HFIP distribution shows the tendency of HFIP to aggregate around the peptide, increasing the local cosolvent concentration to more than two times that in the bulk concentration. The correlation of local peptide structure with HFIP coating suggests that displacement of water at the peptide surface is the main contribution of HFIP in stabilizing the secondary structure of melittin. Finally, a stabilizing effect promoted by the presence of counter-ions was also observed in the simulations.

Keywords: preferential solvation; peptide folding; -helix stability; fluorinated alcohol; cosolvent effect; helix bending

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051426605.

	Introduction

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
1,1,1,3,3,3-Hexafluoro-propan-2-ol (HFIP) is one of the most effective cosolvents for the structural stabilization of secondary structure forming peptides. In particular, it is one of the strongest helix-inducing and stabilizing cosolvents (Hirota et al. 1997). The mechanism of peptide stabilization by fluorinated solvents has been investigated by experimental techniques (Buck 1998) and, more recently, by molecular dynamics simulations (Diaz et al. 2002; Fioroni et al. 2002; Roccatano et al. 2002). The results of these studies have evidenced the presence of a complex mechanism involving a combination of different contributions. In the case of 2,2,2-trifluoroethanol (TFE), computer simulations indicate a coating effect of the cosolvent on the simulated peptides, as a possible mechanism of peptide stabilization (Diaz et al. 2002; Fioroni et al. 2002; Roccatano et al. 2002). The coating effect is favored by the tendency of the fluorinated solvents to form large clusters in aqueous solution (Hong et al. 1999; Gast et al. 2001). The layer of cosolvent around the peptide reduces the accessibility of the backbone hydrogen bonds to the aqueous solvent, improving secondary structure stability.

Among the peptides used to study the effect of fluorinated solvents experimentally, melittin (MLT) is one of the most frequently investigated peptides. Melittin is a 26-residue amphiphilic peptide with sequence GIGA VLKVLTTGLPALISWIKRKRQQ that constitutes one of the principal venom components from the honey bee Apis mellifera. Its toxic effect consists in the lysis of red cells in the blood of the punctured human. In water at low pH and low (< 0.01 M) ion concentration, MLT is monomeric and behaves as a random coil (Kempe et al. 1997). At higher pH, or at higher salt concentration, melittin starts to form monomeric -helices that eventually aggregate to form tetramers. The -helical conformation is induced by the presence of lipid micelles or bilayers, and in this conformation the peptide forms pores in the membrane. Similarly, the addition of cosolvents like HFIP or TFE also induces the formation of -helical structures (Jasanoff and Fersht 1994; Hirota et al. 1997; Kempe et al. 1997; Hong et al. 1999).

The effect of alcoholic solvents or cosolvents on the stability of the melittin -helix has been investigated previously by different authors using molecular simulation methods (Sessions et al. 1998; Fioroni et al. 2001; Roccatano et al. 2002; Liu and Hsu 2003). In simulation studies in methanol (Sessions et al. 1998) and in a membrane environment (Bernèche et al. 1998; Bachar and Becker 2000), melittin stayed close to the experimental -helical structure, whereas in water it starts to bend and unfolds (Roccatano et al. 2002). Short MD simulations (5 nsec) of melittin in 30% (v/v) HFIP/water mixture have already been performed to test the HFIP parameterization (Fioroni et al. 2001). However, this study did not include a systematic analysis of the conformational preference of melittin in HFIP and the molecular mechanism of how HFIP stabilizes the structure of melittin. In a recent article, Gerig (2004) reported an extensive NMR spectroscopic study on the structure of melittin in 35% HFIP/ water mixture. The result of this study indicates the presence of a bent structure with two fluctuating -helices.

In the present study, we perform extensive simulations (100 nsec) of melittin in water and in 35% HFIP/water mixture in order to investigate at the molecular level the structural and dynamic effects of HFIP on this peptide. Furthermore, we also analyzed the effect of counter-ions on the stability of the -helix. The effect of counter-ions on protein stability has been investigated by different authors (Ibragimova and Wade 1998; Sessions et al. 1998; Pfeiffer et al. 1999; Walser et al. 2001). In the case of melittin, an earlier MD simulation in methanol has shown that the presence of counter-ions can produce sensitive effects on structural stability within a few hundred picoseconds (Sessions et al. 1998). The present comparative simulation studies starting from the X-ray structure indicate that melittin rapidly unfolds in water under low pH conditions in agreement with experiment. In 35% HFIP, the helical structure is largely preserved with an average global conformation in good agreement with NMR data. However, the partial unfolding of the helices is seen toward the end of the simulation. Addition of salt slows down the unfolding process both in 35% HFIP and in water. The analysis of the distribution of HFIP molecules around the peptide allows drawing conclusions on the mechanism of structure stabilization by HFIP and the mechanism of helix bending and unfolding.

	Results

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
In Figure 1, the secondary structure analysis of melittin is reported for all the simulations. In the absence of HFIP, the conservation of the helical structure in the course of the simulations depends substantially on the presence or the absence of the counter-ions. The SPC simulation completely loses the helical secondary structure of melittin after 20 nsec, while in SPCi, it remains stable for almost 70 nsec. Interestingly, the C-terminal region is less stable, and at the end of the simulation, it tends to form a -hairpin structure. In the case of HFIP/ water simulations, the peptide shows more defined helical segments during the simulations in the presence and absence of ions. However, in the HFIPi simulation, the -helical regions are longer. The central region of the peptide (residues 9–11) loses its initial helical structure. Interestingly, the structure shows folding/unfolding events of -helical fragments.

View larger version (48K): [in this window] [in a new window]   Figure 1. Time course of the secondary structure for the two simulations. The secondary structure definitions are based on the Kabsch-Sander DSSP definition (Kabsch and Sander 1983).

View larger version (21K): [in this window] [in a new window]   Figure 2. Time average of -helicity per residue of MLT in the four simulations.

View larger version (30K): [in this window] [in a new window]   Figure 3. Time course of the angle between the two helix segments present during the simulations.

View larger version (19K): [in this window] [in a new window]   Figure 4. Time course of the different clusters of structures obtained for the different simulations.

View larger version (29K): [in this window] [in a new window]   Figure 5. Representative structures of the three most populated clusters from the HFIPi and HFIP simulations, respectively.

View larger version (27K): [in this window] [in a new window]   Figure 6. Local HFIP concentration vs. the distance from the C atom of each residue of melittin, calculated for the last 15 nsec of both simulations.

View larger version (23K): [in this window] [in a new window]   Figure 7. Average local HFIP concentration within a distance of 0.6 nm from the C atom of each residue of melittin, calculated using the full trajectory of both simulations. Bars indicate the standard deviations.

View larger version (99K): [in this window] [in a new window]   Figure 8. Snapshots of the last frame of the HFIPi and HFIP simulations. The peptide is represented as ribbon, and the solvent molecules within 0.6 nm are shown. The peptide is oriented with the C-ter at the bottom. Water molecules are represented as dotted surfaces.

	Discussion

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
A number of studies have shown that melittin conformation depends significantly on the solvent environment. In the crystal it adopts a helical structure; in a membrane, a partially helical conformation; and in water, it unfolds. Addition of fluorinated cosolvents can induce the helical structure. Melittin is an excellent model system to systematically study the effect of fluorinated cosolvents on the structure of peptides. The purpose of thisstudy is to analyze the effect of HFIP on the melittin model system using comparative MD simulations on a timescale that goes much beyond any previous simulation on similar systems. At this level of simulation, our 100-nsec MD runs are not long enough to sample with the proper statistical weight folding and unfolding events. Longer simulations or multiple replicas of the trajectories should, in fact, be used to define the broad distribution of conformational first passage times. However, they can give qualitative insight on the interactions of added fluorinated (membrane-mimicking) cosolvents with helical peptides.

The comparative MD simulations indicate that the NOE distance-bound violations, summarized in Table 1, show that both the simulations in 35% HFIPi and HFIP explore regions of conformational space in which the peptide fulfills most of the available NMR-derived constraints. The overall agreement with experimental data is qualitatively good. The observed violations are among the weak-medium NOEs with very few in the medium range. One explanation for the violations could be that in solution, only a fraction of the peptide conformations contribute to some of the experimentally observed NOEs. However, these violations can also be considered as the result of an incomplete sampling of the conformational space accessible to the peptide (Colombo et al. 2002, 2003), and more extended simulations are required to obtain more accurate data. Furthermore, in the case of the HFIP simulation, it is interesting to note that although there is an evident loss of secondary structure detected by the DSSP analysis (Fig. 1), the NOE constraints are still mostly satisfied. The weak correspondence of the secondary structure with the overall folding of the structure was already observed in the simulation of other peptides (Colombo et al. 2002). In the simulations it was also observed that HFIP molecules surrounding the peptides limit the accessibility of water to the surface. A similar behavior was observed for simulations of peptides in TFE/water mixtures (Roccatano et al. 2002). In the case of TFE, this effect was supported by the results of NMR diffusion measurements and MD calculations on other peptides (Diaz et al. 2002; Fioroni et al. 2002). The results of the simulations are in agreement with the model of HFIP aggregation. In the case of the HFIPi simulation, it is possible to distinguish an inhomogeneous coating of the HFIP around the peptide. The presence of microhetero-geneity of the HFIP/water mixture has been evidenced by light scattering data (Kuprin et al. 1995; Hong et al. 1999; Gast et al. 2001) and theoretical MD calculations (Fioroni et al. 2001). The clustering effect was also proposed by Gerig (2004) to give an interpretation of the NMR cross-relaxation rate measurements. Using a simplified model that accounts for the aggregation of the HFIP molecules in water, it results in a local concentration of HFIP around the peptide of 1.6 times the bulk concentration. Our results show that the averagelocal concentration (76% [v/v]) can be compared with this estimation, providing further microscopic evidence to the stabilization mechanism of fluorinated solvents.

The present simulations indicate that accumulation of HFIP around melittin is site-specific. The HFIP concentration around -helical peptide regions is higher than in regions of irregular peptide backbone (near the kink or the ends of the peptide). Similar to TFE (Roccatano et al. 2002), HFIP molecules aggregate around the solute preventing the formation of hydrogen bonds with water molecules that can disrupt the -helix structure (Pande et al. 1998; Walgers et al. 1998). The interactions between the peptide and HFIP do not displace the peptide–peptide interactions that stabilize the secondary structure. In the case of HFIP, the large molecular size can further deplete the possible interactions of HFIP with the backbone melittin atoms, enhancing the -helix stabilization.

The origins of the stabilization mechanism may thus be both entropic and enthalpic. We noticed that the hydrophobic cosolvent tends to cluster around peptide regions rich in hydrophobic side chains. This effect tends to displace ordered water molecules from the vicinities of both HIFP and hydrophobic side chains, with a clear entropic gain for the final configuration of the system. Moreover, once water is excluded from the immediate vicinity of the peptide, intra-molecular hydrogen bonds can form and stabilize, yielding a net favorable energetic contribution. Although, as stated above, the simulations are still too short to determine these effects quantitatively, the qualitative picture points to a combination of factors favoring peptide coating by HIFP.

It is also interesting to note the very good correspondence (residues 9–11; = 77°) of the angular kink observed in the simulation with the NMR-determined structures (Gerig 2004). Furthermore, the formation of -helix hairpin structure with a similar angular kink was observed in a theoretical study of melittin in the presence of POPC lipid bilayer (Lin and Baumgaertner 2000), but in the DPPC and DMPC lipid bilayer, a more extended structure was observed (Bernèche et al. 1998; Bachar and Becker 2000). In the last two cases, the simulation length was, however, limited to 500 psec. Our MD study indicates that the angle between helical segments is not static but can adopt a wide range of values. This might be of functional importance for the mechanism of membrane binding and insertion. Finally, the present comparative MD simulations also indicate a secondary-structure-stabilizing effect induced by the presence of counter-ions. In water the presence of counter-ions slows down the decay of secondary structure of melittin. Although this effect may be a purely kinetic effect (longer simulation may lead to a similar decay effect as seen in water), it is in qualitative agreement with experimental data. In fact, high salt concentrations and low pH increase the presence of -helices in the tetrameric melittin form (Brown et al. 1980; Iwadate et al. 1998). In case of the HFIP mixture simulations, salt concentration still plays an important role. In fact, in the case of HFIP simulation, although to a lesser extent, the secondary structure is lost in the course of the simulation. However, the presence of HFIP retards the loss of secondary structure, extending the lifetime of the -helix over a longer timescale than in pure water simulation (SPC).

	Conclusions

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
In this study, we have used molecular dynamics simulations to analyze the effect of HFIP on the stability of the melittin peptide. The structural data evidence a very good correspondence with the experimental NMR data. The inclusion of counter-ions partly enhances the stability of the helical peptide structure, in agreement with experimental observations. Furthermore, the simulations show that in a HFIP/water mixture the organic cosolvent aggregates around the peptide, forming a matrix that partly excludes water. The nonuniform distribution of the HFIP around the peptide, supports the hypothesis of the presence of HFIP clusters that interact with the peptide. This, in turn, promotes the formation of local interactions and, as a consequence, ordered secondary structure. By displacing water from the surface, HFIP has several effects: First, it removes alternative hydrogen-bonding partners and, second, it provides a low dielectric environment. Together, these factors favor the formation of intrapeptide hydrogen bonds. The results are in line with previous simulation studies with TFE/ water mixture, indicating a similar coating effect that promotes secondary structure stabilization.

	Materials and methods

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
The starting conformation for the simulations of the melittin peptide was taken from the 0.2-nm-resolution crystal structure (PDB entry 2MLT [PDB] ) (Anderson et al. 1980). The peptide was protonated according to the experimental conditions (pH 2). The C-terminal residue was aminated. The peptide was centered in a cubic box and solvated with SPC water (Berendsen et al. 1987) or with a mixture of SPC water and HFIP molecules. We have used 3000 water molecules for the pure water simulations, and 4000 water and 350 HFIP molecules for the 35% (v/v) HFIP mixture. All solvent molecules with any atom within 0.15 nm of the peptide were removed. The concentration of the HFIP/SPC water mixture corresponds approximately to 35% v/v.

For the simulations with counter-ions (abbreviated SPCi and HFIPi for the water and HFIP/water mixture, respectively), six Cl^– counter-ions were added to neutralize the total charge of the systems. This was achieved by replacing water molecules at the most positive potential. The abbreviations SPC and HFIP will be used to indicate the simulations in water and HFIP/water mixture, respectively. The GROMOS96 force field (van Gunsteren et al. 1996) was used to describe the peptide. For the HFIP, the model proposed by Fioroni et al. (2001) was used. This model was optimized to reproduce the physicochemical properties of the pure liquid and mixtures with water. The model has been found in good agreement with the experimental data based on X-ray, neutron scattering, and NMR of the pure liquid as well as the mixtures (Yoshida et al. 2003).

All the systems were initially energy-minimized with the steep est descent method for 1000 steps. During the MD simulations, the peptide and the rest of the system were coupled separately to the temperature bath. The temperature was maintained close to the intended values (300 K) by weak coupling to an external temperature bath using a coupling time _T = 0.1 psec (Berendsen et al. 1984). The pressure was kept constant at P₀ = 1 by weak coupling to a bath of constant pressure with a coupling time _P = 0.5 psec (Berendsen et al. 1984). The LINCS algorithm (Hess et al. 1997) was used to constrain all bond lengths. For the water molecules, the SETTLE algorithm (Miyamoto and Kollman 1992) was used. A relative dielectric permittivity, _r = 1, and a time step of 2 fsec were used. A twin-range cutoff was used for the calculation of the nonbonded interactions. The short-range cutoff radius was set to 0.8 nm and the long-range cutoff radius, to 1.4 nm, for both Coulombic and Lennard-Jones interactions. No reaction field corrections beyond the long-range cutoff were included in the cutoff simulations. Interactions within the short-range cutoff were updated every time step, whereas interactions within the long-range cutoff were updated every five time steps together with the pair-list.

All atoms were given an initial velocity obtained from a Maxwellian distribution at the desired initial temperature. All the simulations were equilibrated by 50 psec of MD runs with positional restraints on the peptide to allow the relaxation of the solvent molecules. These first equilibration runs were followed by another 50-psec run without position restraints on the peptide. The production runs, after equilibration, were 100 nsec long.

Analysis of the simulations
The secondary structure of the peptides was analyzed using the DSSP criteria (Kabsch and Sander 1983). The -helicity was calculated using the criterion of Hirst and Brooks (1995). Cluster analysis was performed using the Jarvis-Patrick method (Jarvis and Patrick 1973): A structure is added to a cluster when this structure and a structure in the cluster have each other as neighbors and they have at least P neighbors in common. The neighbors of a structure are the M closest structures or all the structures within a cutoff, based on the root mean square deviation between backbone atoms. In our case, P was 3, M was 10, and the RMSD was 0.1 nm.

The angle between helical axes was calculated using the MOLMOL program (Koradi et al. 1996). For each simulation frame, the boundary residues of the two helices are evaluated and used to perform the calculation of the helical axes. The interproton distances were calculated from the simulations as r^–6–1/6 averages (Tropp 1980).

The concentration (% v/v) of HFIP molecules around the peptide residues, named local HFIP concentration (LHC), was evaluated from the cumulative number of water [n_w(r)] and HFIP [n_H(r)] molecules present within a distance r from the Cs of the single residues using the following relation:

(1)

where V_m^H = 0.1 and V_m^w = 0.019 L/mol are the average excluded volumes for HFIP and water molecules, respectively (Marcus 1998). All the MD runs and the analysis of the trajectories were performed using the GROMACS software package (Berendsen et al. 1995; Lindahl et al. 2001).

	References

TOP Abstract Introduction Results Discussion Conclusions Materials and methods References

 
Anderson, D., Terwilliger, T.C., Wickner, W., and Eisenberg, D. 1980. Melittin forms crystals which are suitable for high resolution X-ray structural analysis and which reveal a molecular 2-fold axis of symmetry. J. Biol. Chem. 255: 2578–2582.[Abstract/Free Full Text]

Bachar, M. and Becker, O.M. 2000. Protein-induced membrane disorder: A molecular dynamics study of melittin in a dipalmitoylphosphatidyl-choline bilayer. Biophys. J. 78: 1359–1375.[Abstract/Free Full Text]

Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Di Nola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684–3690.[CrossRef]

Berendsen, H.J.C., Grigera, J.R., and Straatsma, T.P. 1987. The missing term in effective pair potentials. J. Phys. Chem. 91: 6269–6271.[CrossRef]

Berendsen, H.J.C., van der Spoel, D., and van Drunen, R. 1995. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91: 43–56.[CrossRef]

Bernèche, S., Nina, M., and Roux, B. 1998. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys. J. 75: 1603–1618.[Abstract/Free Full Text]

Brown, L.R., Lauterwein, J., and Wüthrich, K. 1980. High-resolution ¹HNMR studies of self-aggregation of melittin in aqueous solution. Biochim. Biophys. Acta 622: 231–244.[Medline]

Buck, M. 1998. Trifluoroethanol and colleagues: Cosolvents come of age. Recent studies with peptides and proteins. Quart. Rev. Biophys. 31: 297–355.[CrossRef][Medline]

Colombo, G., Roccatano, D., and Mark A.E. 2002. Folding and stability of the three-stranded -sheet peptide nova: Insights from molecular dynamics simulations. Proteins 46: 380–392.[CrossRef][Medline]

Colombo, G., De Mori, G.M.S., and Roccatano, D. 2003. Interplay between hydrophobic cluster and loop propensity in -hairpin formation: A mechanistic study. Protein Sci. 12: 538–550.[Abstract/Free Full Text]

Diaz, M.D., Fioroni, M., Burger, K., and Berger, S. 2002. Evidence of complete hydrophobic coating of bombesin by trifluoroethanol in acqueous solution: An NMR spectroscopic and molecular dynamics study. Chem. Eur. 8: 1663–1669.

Fioroni, M., Burger, K., Mark, A.E., and Roccatano, D. 2001. A model of 1,1,1,3,3,3-hexafluoropropan-2-ol for molecular dynamics simulations. J. Phys. Chem. B 105: 10967–10975.[CrossRef]

Fioroni, M., Diaz, M.D., Burger, K., and Berger, S. 2002. Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures: A diffusion NMR, interolecular NOE and molecular dynamics study. J. Am. Chem. Soc. 124: 7737–7744.[CrossRef][Medline]

Gast, K., Siemer, A., Zirwer, D., and Damaschun, G. 2001. Fluoroalcohol-induced structural changes in proteins: Some aspects of cosolvent– protein interactions. Eur. Biophys. J. 30: 273–283.[CrossRef][Medline]

Gerig, J.T. 2004. Structure and solvation of melittin in 1,1,1,3,3,3-hexafluoro- 2-propanol/water. Biophys. J. 86: 3166–3175.[Abstract/Free Full Text]

Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. 1997. LINCS: A linear constraint solver for molecular simulations. J. Comp. Chem. 18: 1463–1472.[CrossRef]

Hirota, N., Mizuno, K., and Goto, Y. 1997. Cooperative -helix formation of -lactoglobulin and melittin induced by hexafluoroisopropanol. Protein Sci. 6: 416–421.[Abstract]

Hirst, J.D. and Brooks, C.L. 1995. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34: 7614–7621.[CrossRef][Medline]

Hong, D.-P., Hoshino, M., Kuboi, R., and Goto, Y. 1999. Clustering of fluorine-substituted alcohols as a factor responsible for their marked effects on proteins and peptides. J. Am. Chem. Soc. 121: 8427–8433.[CrossRef]

Ibragimova, G.T. and Wade, R.C. 1998. Importance of explicit salt ions for protein stability in molecular dynamics simulation. Biophys. J. 74: 2906–2911.[Abstract/Free Full Text]

Iwadate, M., Asakura, T., and Williamson, M.P. 1998. The structure of the melittin tetramer at different temperatures. An NOE-based calculation with chemical shift refinement. Eur. J. Biochem. 257: 479–487.[Medline]

Jarvis, R.A. and Patrick, E.A. 1973. Clustering using a similarity measure based on shared near neighbors. IEEE Trans Comp. 22: 1025–1034.

Jasanoff, A. and Fersht, A. 1994. Qualitative determination of helical propensities from trifluoroethanol titration curves. Biochemistry 33: 2129– 2135.[CrossRef][Medline]

Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2576–2637.

Kempe, M.D., Buckley, P., Yuan, P., and Prendergast, F.G. 1997. Main chain and side chain dynamics of peptides in liquid solution from ¹³C NMR: Melittin as a model peptide. Biochemistry 36: 1678–1688.[CrossRef][Medline]

Koradi, R., Billiter, M., and Wültrich, K. 1996. MOLMOL: A program for display and analysis of molecular structures. J. Mol. Graph. 14: 51–55.[CrossRef][Medline]

Kuprin, S., Grauslund, A., Ehrenberg, A., Koch, M.H.J., and Horn, M.I. 1995. Nonideality of water–hexafluoropropanol mixtures as studied by X-ray small angle scattering. J. Biochem. Biophys. Res. Comm. 217: 1151–1156.

Lin, J.H. and Baumgaertner, A. 2000. Molecular dynamics simulations of hydrophobic and amphiphatic proteins interacting with a lipid bilayer membrane. Comp. Theor. Polymer Sci. 10: 97–102.[CrossRef]

Lindahl, E., Hess, B., and van der Spoel, D. 2001. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7: 306–317.

Liu, H.L. and Hsu, C.-M. 2003. The effect of solvent and temperature on the structural integrity of monomeric melittin by molecular dynamics simulations. Chem. Phys. Lett. 375: 119–125.[CrossRef]

Marcus, Y. 1998. The properties of solvents. Wiley Series in Solution Chemistry, Vol. 4. John Wiley, Chichester-New York.

Miyamoto, S. and Kollman, P.A. 1992. SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comp. Chem. 13: 952–962.[CrossRef]

Pande, V.S., Grosberg, A.Y., Tanake, T., and Rokhsar, D.S. 1998. Pathways for protein folding: Is a new view needed? Curr. Opin. Struct. Biol. 8: 68–79.[CrossRef][Medline]

Pfeiffer, S., Fushman, D., and Cowburn, D. 1999. Impact of Cl^– and Na⁺ ions on simulated structure and dynamics of ark1 ph domain. Proteins 35: 206–217.[CrossRef][Medline]

Roccatano, D., Colombo, G., Fioroni, M., and Mark, A.E. 2002. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary- structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci. 99: 12179–12184.[Abstract/Free Full Text]

Sessions, R.B., Gibbs, N., and Dempsey, C.E. 1998. Hydrogen bonding in helical polypeptides from molecular dynamics simulations and amide hydrogen exchange analysis: Alamethicin and melittin in methanol. Biophys. J. 74: 138–152.[Abstract/Free Full Text]

Tropp, J. 1980. Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J. Chem. Phys. 72: 6035–6043.[CrossRef]

van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., and Tironi, I.G. 1996. Biomolecular simulation: The GROMOS96 manual and user guide. Hochschulverlag AG an der ETH Zürich, Zürich.

Walgers, R., Lee, T.C., and Cammers-Goodwin, A. 1998. An indirect chaotropic mechanism for the stabilization of helix conformation of peptides in aqueous trifluoroethanol and hexafluoro-2-propanol. J. Am. Chem. Soc. 120: 5073–5079.[CrossRef]

Walser, R., Hünenberger, P.H., and van Gunsteren, W.F. 2001. Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins 44: 509–519.[CrossRef]

Yoshida, K., Yamaguchi, T., Adachi, T., Otomo, T., Matsuo, D., Takamuku, T., and Nishi, N. 2003. Structure and dynamics of hexafluoroisopropanol– water mixtures by X-ray diffraction, small-angle neutron scattering, NMR spectroscopy, and mass spectrometry. J. Chem. Phys. 119: 6132–6142.[CrossRef]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				S. Tanizaki, J. Clifford, B. D. Connelly, and M. Feig Conformational Sampling of Peptides in Cellular Environments Biophys. J., February 1, 2008; 94(3): 747 - 759. [Abstract] [Full Text] [PDF]

				G. Wei and J.-E. Shea Effects of Solvent on the Structure of the Alzheimer Amyloid-{beta}(25-35) Peptide Biophys. J., September 1, 2006; 91(5): 1638 - 1647. [Abstract] [Full Text] [PDF]

This Article Abstract Full Text (PDF) All Versions of this Article: ps.051426605v1 14/10/2582    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Roccatano, D. Articles by Colombo, G. Search for Related Content PubMed PubMed Citation Articles by Roccatano, D. Articles by Colombo, G. Social Bookmarking                   What's this?