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The Solvation Interface Is a Determining Factor in Peptide Conformational Preferences

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The Solvation Interface Is a Determining Factor in Peptide Conformational Preferences doi:10.1016/j.jmb.2005.11.058 J. Mol. Biol. (2006) 356, 248–256 The Solvation Interface is a Determining Factor in Peptide Conformational Preferences Eric J. Sorin1, Young Min Rhee4, Michael R. Shirts5 and Vijay S. Pande1,2,3* 1 Department of Chemistry The 21 residue polyalanine-based Fs peptide was studied using thousands Stanford University, Stanford of long, explicit solvent, atomistic molecular dynamics simulations that CA 94305-5080, USA reached equilibrium at the ensemble level. Peptide conformational preference as a function of hydrophobicity was examined using a spectrum 2Department of Structural of explicit solvent models, and the peptide length-dependence of the Biology, Stanford University hydrophilic and hydrophobic components of solvent-accessible surface Stanford, CA 94305-5080 area for several ideal conformational types was considered. Our results USA demonstrate how the character of the solvation interface induces several 3Stanford Synchrotron conformational preferences, including a decrease in mean helical content Radiation Laboratory, Stanford with increased hydrophilicity, which occurs predominantly through University, Stanford, CA reduced nucleation tendency and, to a lesser extent, destabilization of 94305-5080, USA helical propagation. Interestingly, an opposing effect occurs through 4 increased propensity for 310-helix conformations, as well as increased Department of Chemistry polyproline structure. Our observations provide a framework for under- University of California at standing previous reports of conformational preferences in polyalanine- Berkeley, Berkeley, CA 94720 based peptides including (i) terminal 310-helix prominence, (ii) low p-helix USA propensity, (iii) increased polyproline conformations in short and unfolded 5Department of Chemistry peptides, and (iv) membrane helix stability in the presence and absence of Columbia University, New York water. These observations provide physical insight into the role of water in NY 10027, USA peptide conformational equilibria at the atomic level, and expand our view of the complexity of even the most “simple” of biopolymers. Whereas previous studies have focused predominantly on hydrophobic effects with respect to tertiary structure, this work highlights the need for consideration of such effects at the secondary structural level. q 2005 Elsevier Ltd. All rights reserved. Keywords: protein folding; explicit solvent; distributed computing; *Corresponding author hydrophobicity; molecular dynamics Introduction behaviors, a predominant theme in contemporary theories is that of hydrophobicity and hydro- The protein folding problem has garnered much philicity,1 and several studies have been published attention over the past few decades. At the most recently that examine the role of water in self- fundamental level, folding is defined by the assembly.2–13 underlying distribution of thermodynamic states, It is intuitive to assume that the conformational both stable and otherwise, that determine the preferences of a given protein or peptide are interesting and experimentally detectable features influenced significantly by local environmental ofthefreeenergylandscape,aswellasthe conditions, and the most important environmental measurable kinetic modes of conformational condition is the character of the surrounding change. While it is accepted that many factors solvent. More specifically, we refer herein to the contribute to experimentally observed folding solvation interface, which communicates bulk properties of the solvent (i.e. temperature, pressure, dielectric/salt effects) to the peptide and deter- Abbreviations used: RMS, root-mean-squared; LR, mines localized effects about the peptide due to Lifson–Roig. specific solute–solvent interactions (i.e. hydro- E-mail address of the corresponding author: phobic, water-mediated, and ion-binding inter- [email protected] actions). Understanding how the solvation 0022-2836/$ - see front matter q 2005 Elsevier Ltd. All rights reserved. Solvation Interface and Peptide Conformation 249 interface affects peptide conformational preferences appreciated that solvent effects play an important is thus a fundamental concept in current and future role in peptide and protein structure:1 it is well efforts to understand and model the protein folding established that polyalanine is helix-stabilizing,22,23 problem on the residue and atomic scales. that charged blocking groups stabilize even “short” Although gaining experimental insight into the polyalanine helices in aqueous solvent,24 and that effects of solvation on protein folding remains a the hydrophobic effect plays a significant role in challenge,14 a new era of computational power and helix stability.25,26 Herein, we consider the molecu- complexity now allows the simulation of protein lar basis of the effect of hydrophobicity on peptide dynamics in all-atom detail using explicit represen- conformation. Indeed, a number of conformational tations of aqueous solvent. In many ways, such types are known within the “helical spectrum,” efforts began with the seminal work by Duan and which includes a,310, p, and polyproline regions of Kollman, whose 1 ms explicit solvent simulation of the Ramachandran map, and preferences toward the villin headpiece15 set the stage for simulating each of these specific forms of helix have been protein conformational change in all-atom detail. identified, as discussed below. This study serves as More recently, Zhou et al. reported on hydrophobic the first to probe the connection between those collapse between two domains of the BphC enzyme, preferences and the character of the solvent. We demonstrating a dependence of the observed have identified a clear correlation between such hydrophobic collapse kinetics upon solute–solvent structural preferences and the strength of the electrostatic interactions.5 Rhee et al. studied hydrophobic effect, and the observed conformation- complete folding of the BBA5 mini-protein in al response to hydrophobicity rationalizes the explicit solvent using ensemble dynamics method- complex conformational preferences observed in ology,16 describing water-induced effects not cap- simple polyalanine-based peptides. tured by implicit solvation models, including a Shirts and Pande recently showed that minor concurrent core collapse and desolvation mechan- modifications to the TIP3P water model27 decrease ism,9 and we recently reported a similar need for the mean error in hydration free energies of explicit solvation in simulations of the folding of a common amino acid sidechain analogs to 0.0G small RNA.8 0.1 kcal/mol while reducing the root-mean-squared While these and other recent works have shown (RMS) error below that of any of the published the utility of simulation in furthering our under- water models tested, with measured bulk liquid standing of the effects of solvation on configura- water properties remaining almost constant.28 tional preferences, the limiting factor in To consider the effect of the solvation interface on contemporary simulation studies is most often protein conformational preference in a simple and that of sampling true equilibrium. We have recently systematic way, we therefore examine the equili- reported true ensemble-level equilibrium sampling brium thermodynamics of the Fs peptide in a of the capped 21 residue a-helical Fs peptide in spectrum of water models including TIP3P, TIP3P- all-atom detail,17,18 using Folding@Home, a world- MOD,29 and the six TIP3P-M2X models described wide distributed computing network.19 The previously28 and outlined in Table 1. A recent study sampling reported in our previous studies,17,18 by Rose and co-workers showed that solvation orders of magnitude greater than the experimental free energy in TIP3P explicit solvent simulations folding time, allowed us to assess several contem- correlated strongly with the interaction energy porary protein potentials including AMBER-94, between the peptide and coordinated (i.e. first AMBER-96, AMBER-99, and AMBER-GS (modified shell) water molecules.30 With this in mind, we AMBER-94 of Garcia and Sanbonmatsu), as well as conducted a computational thought experiment in a new variant dubbed AMBER-99f, which reduces which the solute–solvent interaction energy barriers along the f torsion in AMBER-99, thereby is varied by employing the eight TIP3P variants making helical conformations more accessible to the listed above, thereby studying the effects of peptide. While both the original and modified “hydrophobic titration” on peptide conformational versions of AMBER-94 exhibited significant helix- equilibrium. friendly equilibria, and the AMBER-96 and In the solvent models listed above, the energetic AMBER-99 force fields favored extended non- benefit of forming close van der Waals contact helical conformations, the AMBER-99f potential between solute and solvent is increased by was shown to yield the strongest agreement with increasing the Lennard-Jones potential well experimental measurements on this system, includ- depth, 3,byw65%. To compensate for the increase ing folding rate, Lifson–Roig (LR) parameters, and in atomic repulsion at a given distance, the radius of gyration.17 The notable agreement with Lennard-Jones radius, s, is decreased to maintain several experiments, the ability to simulate this the experimental density of water, with changes of system to true equilibrium, and the fact that a-helices %1.5% in the optimal oxygen–oxygen separation. compose the most elementary subunits of protein These changes thus allow the bulk character
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