Peptides In Solvents Research Articles

Simulations of the pressure and temperature unfolding of an alpha-helical peptide.

We study by molecular simulations the reversible folding/unfolding equilibrium as a function of density and temperature of a solvated alpha-helical peptide. We use an extension of the replica exchange molecular dynamics method that allows for density and temperature Monte Carlo exchange moves. We studied 360 thermodynamic states, covering a density range from 0.96 to 1.14 g.cm(-3) and a temperature range from 300 to 547.6 K. We simulated 10 ns per replica for a total simulation time of 3.6 micros. We characterize the structural, thermodynamic, and hydration changes as a function of temperature and pressure. We also calculate the compressibility and expansivity of unfolding. We find that pressure does not affect the helix-coil equilibrium significantly and that the volume change upon pressure unfolding is small and negative (-2.3 ml/mol). However, we find significant changes in the coordination of water molecules to the backbone carbonyls. This finding predicts that changes in the chemical shifts and IR spectra with pressure can be due to changes in coordination and not only changes in the helical content. A simulation of the IR spectrum shows that water coordination effects on frequency shifts are larger than changes due to elastic structural changes in the peptide.

Theoretical Study of the Thermodynamics of a Solvated Peptide: Contryphan Vn

In recent papers we combined molecular dynamics (MD) simulations with the quasi Gaussian entropy (QGE) theory, in order to model the statistical mechanics and thermodynamics of simple solute molecules in water. In this paper we apply this approach to a more complex solute in water: a 9 residues peptide, Contryphan Vn. Results show that this approach can provide an accurate theoretical description of this complex solute-solvent system over a wide range of temperature.

Effects of H2O and D2O on Polyproline II Helical Structure

The interaction of solvent with a polypeptide chain is one of the primary factors controlling protein folding and stability. In biologically relevant systems, this solvent is most often water. Experimental estimates of the role of water in peptide folding can be obtained from solvent perturbation experiments. The simplest perturbant for H2O water is its isotopic D2O form. The solvation of peptides known to form PII helices with D2O versus H2O increases their propensity to adopt the PII conformation.

Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules.

Origin of the neighboring residue effect on peptide backbone conformation.

Unfolded peptides in water have some residual structure that may be important in the folding process, and the nature of the residual structure is currently of much interest. There is a neighboring residue effect on backbone conformation, discovered in 1997 from measurements of (3)J(HN alpha) coupling constants. The neighboring residue effect appears also in the "coil library" of Protein Data Bank structures of residues not in alpha-helix and not in beta-structure. When a neighboring residue (i - 1 or i + 1) belongs to class L (aromatic and beta-branched amino acids, FHITVWY) rather than class S (all others, G and P excluded), then the backbone angle of residue i is more negative for essentially all amino acids. Calculated values of peptide solvation (electrostatic solvation free energy, ESF) predict basic properties of the neighboring residue effect. We show that L amino acids reduce the solvation of neighboring peptide groups more than S amino acids. When tripeptides from the coil library are excised to allow solvation, the central residues have more negative values of <phi> but less negative values of <ESF> with L than with S neighbors. The coil library values of <(3)J(HN alpha)>, which vary strikingly among the amino acids, are correlated with the neighboring residue effect seen by ESF. Moreover, values for the "blocking effect" of side chains on the hydrogen exchange rates of peptide NH protons are correlated with ESF values.

Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm

This chapter discusses the atomic simulations of protein folding, using the replica exchange (RE) algorithm. In REs method, several copies or replicas of a system are simulated in parallel, only occasionally exchanging temperatures through a Monte Carlo (MC) move that maintains detailed balance. This algorithm is ideal for a large cluster of poorly communicating processors because temperature exchanges can be relatively infrequent and require little data transfer. It was adapted for use with molecular dynamics and named the replica exchange molecular dynamics (REMD) method. The essence of the REMD method is to use the molecular dynamics to generate a suitable canonical ensemble in each replica rather than MC. REMD normally occurs in coordinate and momentum space instead of just coordinate space. The typical temperature fluctuations and their relation to conformational changes are demonstrated from an actual REMD simulation of a solvated peptide. The use of REMD to study the thermodynamics of helix-coil transitions in peptides that are experimentally characterized is also elaborated.

A microscopic view of peptide and protein solvation

The structure and dynamics of the water hydrating peptides and proteins are examined here at atomic resolution via molecular dynamics simulations. Detailed solvation density and residence time data for all 20 l-amino acids in an end-capped AXA tripeptide motif are presented. In addition, the solvation of the protein chymotrypsin inhibitor 2 is investigated as a point of comparison. Residues on the surface of proteins are not isolated; they interact both locally and non-locally in sequence space, and comparison of the solvation properties of each amino acid in both the peptide and protein allow us to distinguish inherent solvation properties from context-dependent perturbations due to neighboring residues. This work moves beyond traditional radial distribution functions and presents graphical representations of preferential solvation and orientation of water by side chains and the main chain. The combination of 0.3 μs of simulation data improves the statistical sampling over previous studies and reveals the significance of bridging water molecules that stabilize and mediate side chain–side chain, side chain–main chain and main chain–main chain interactions at the solvation interface.

Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules

Methods by which to determine conditions for a molecular dynamics (MD) simulation of biological molecules were investigated. Derivation of the optimal parameters of the Ewald summation was described so as to give same precision to the real space, the reciprocal space summations and the van der Waals interaction. Later, the procedure by which to determine the condition of the multiple time step method by RESPA (REference System Propagator Algorithm; Tuckerman et al., 1992, J. Chem. Phys., 97, 1990) was described as exemplified by MD simulations of a solvated β-sheet peptide. The conservation of the total energy in a microcanonical ensemble was measured to investigate the stability of the simulation conditions. The most feasible respective combinations of the time steps were: 0.25 fs for bond, angle and torsion interactions; 2 fs for van der Waals interaction and Ewald real-space summation; and 4 fs for Ewald reciprocal-space summation. Though it retained an acceptable accuracy, this condition accelerated the simulation ten-fold compared to that in which a simple velocity-Verlet method with a time step of 0.25 fs was used. The update of the correction term due to excluded neighbors was then investigated. Better results were obtained when the correction was updated with the real-space than when it was updated with the reciprocal-space summation. Finally, an MD simulation as long as 50 ps performed under the optimal Ewald and RESPA parameters was thus determined. The trajectory showed a good stability, indicating the feasibility of the parameters.

An improved method of preparing the amyloid β-protein for fibrillogenesis and neurotoxicity experiments

Synthetic amyloid β-protein (Aβ) is used widely to study fibril formation and the physiologic effects of low molecular weight and fibrillar forms of the peptide on cells in culture or in experimental animals. Not infrequently, conflicting results have arisen in these studies, in part due to variation in the starting conformation and assembly state of Aβ. To avoid these problems, we sought a simple, reliable means of preparing Aβ for experimental use. We found that solvation of synthetic peptide with sodium hydroxide (AβNaOH), followed by lyophilization, produced stocks with superior solubility and fibrillogenesis characteristics. Solubilization of the pretreated material with neutral buffers resulted in a pH transition from -10.5 to neutral, avoiding the isoelectric point of Aβ (pl=5.5), at which Aβ precipitation and aggregation propensity are maximal. Relative to trifluoroacetate (Aβ-TFA) or hydrochloric acid (Aβ-HCl) salts of Aβ, yields of “low molecular weight Aβ” (monomers and/or dimers) were improved significantly by NaOH pretreatment. Time-dependent changes in circular dichroism spectra and Congo red dye-binding showed that Aβ-NaOHformed fibrils more readily than did the other Aβ preparations and that these fibrils were equally neurotoxic. NaOH pretreatment thus offers advantages for the preparation of Aβ for biophysical and physiologic studies.

Fluoroalcohols as structure modifiers in peptides and proteins: hexafluoroacetone hydrate stabilizes a helical conformation of melittin at low pH.

The effect of hexafluoroacetone hydrate (HFA) on the structure of the honey bee venom peptide melittin has been investigated. In aqueous solution at low pH melittin is predominantly unstructured. Addition of HFA at pH approximately 2.0 induces a structural transition from the unstructured state to a predominantly helical conformation as suggested by intense diagnostic far UV CD bands. The structural transition is highly cooperative and complete at 3.6 M (50% v/v) HFA. A similar structural transition is also observed in 2,2,2 trifluoroethanol which is complete only at a cosolvent concentration of approximately 8 M. Temperature dependent CD experiments support a 'cold denaturation' of melittin at low concentrations of HFA, suggesting that selective solvation of peptide by HFA is mediated by hydrophobic interactions. NMR studies in 3.6 M HFA establish a well-defined helical structure of melittin at low pH, as suggested by the presence of strong NH/NHi+1 NOEs throughout the sequence, along with many medium range helical NOEs. Structure calculations using NOE-driven distance constraints reveal a well-ordered helical fold with a relatively flexible segment around residues T10-G11-T12. The helical structure of melittin obtained at 3.6 M HFA at low pH is similar to those determined in methanolic solution and perdeuterated dodecylphosphocholine micelles. HFA as a cosolvent facilitates helix formation even in the highly charged C-terminal segment.

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points.

Use Of 1-β-Naphthalenesulfonyloxybenzotriazole As Coupling Reagent For Peptide Synthesis In The Presence Of Fluorinated Alcohols As Cosolvent

Abstract: Solution Phase synthesis of peptides in solvents mixed with fluorinated alcohols have been carried out using 1-B-Naphthalenesulfonyloxybenzotriazole (NSBt) as coupling reagent.

Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy contributions are calculated using the ECEPP/3 force field model. In considering the effects of hydration, two implicit free energy models are compared. One method is based on the calculation of solvent-accessible surface areas, while the other uses information on the solvent-accessible volume of hydration shells. Detailed information on the potential and solvation energy contributions is presented for the terminally blocked single residue peptides. In addition, based on a procedure that allows the exclusion of domains of the (φ, ψ) space, a number of oligopeptide structure prediction problems are considered, and the role of the solvation model in defining global minimum conformations is addressed.

Molecular Dynamics Simulations of Cyclic and Linear DPDPE: Influence of the Disulfide Bond on Peptide Flexibility

Three 1 ns simulations of the solvated DPDPE peptide have been performed, one for the cyclic and two for the linear forms. The trajectories allow us to describe the conformations explored by DPDPE and DPDPE(SH)2 in aqueous solution on the 1 ns time scale, to quantify the conformational constraints imposed by the presence of the disulfide bond by comparing the conformational flexibility of the cyclic and acyclic peptides, evaluate several physical properties (NMR vicinal coupling constants, diffusion coefficients, and dipole moments of the peptides), and to suggest relations between the calculated properties and biological function. The cyclic peptide, while retaining the general structural features found previouslythe presence of a hydrophobic and a hydrophilic face and a parallel arrangement of peptide dipoles, explores four major conformers during the 1 ns simulation. In two independent simulations, started from an extended and a cycliclike structure, the linear peptide is found to be about twice as str...

Template assisted protein de novo design

Abstract

High-performance liquid chromatographic purification of extremely hydrophobic peptides: transmembrane segments.

Transmembrane peptides of integral membrane proteins often exhibit extremely high hydrophobicity. Therefore, the solubility of such peptides in solvents commonly used in HPLC is usually very low and the interaction with generally applied stationary phases such as silica gel or C18 reversed phases appears to be extremely strong, which makes the characterization and purification of these peptides difficult. The analytical characterization and preparative separation of the synthesized M1 transmembrane sequence of the inhibitory glycine receptor M(r) 48,000 subunit and some of its fragments is shown. M1 and its larger fragments could be dissolved in a dichloromethane-hexafluoro-2-propanol mixture containing a trace amount of pyridine for their separation on a C4 phase by employing linear two-component gradients of formic acid-2-propanol and formic acid-water with ratios up to 4:1 (v/v). Conditions to avoid formylation of the peptides are indicated.

PVM‐AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters

AbstractA parallel version of the popular molecular mechanics package AMBER suitable for execution on workstation clusters has been developed. Computer‐intensive portions of molecular dynamics or free‐energy perturbation computations, such as nonbonded pair list generation or calculation of nonbonded energies and forces, are distributed across a collection of Unix workstations linked by Ethernet or FDDI connections. This parallel implementation utilizes the message‐passing software PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory to coordinate data exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid bilayer systems indicate that reasonable parallel efficiency (70–90%) and computational speedup (2–5 × serial computer runtimes) can be achieved with small workstation clusters (typically six to eight machines) for typical biomolecular simulation problems. PVM‐AMBER is also easily and rapidly portable to different hardware platforms due to the availability of PVM for numerous computers. The current version of PVM‐AMBER has been tested successfully on Silicon Graphics, IBM RS6000, DEC ALPHA, and HP 735 workstation clusters and heterogeneous clusters of these machines, as well as on CRAY T3D and Kendall Square KSR2 parallel supercomputers. Thus, PVM‐AMBER provides a simple and cost‐effective mechanism for parallel molecular dynamics simulations on readily available hardware platforms. Factors that affect the efficiency of this approach are discussed. © 1995 by John Wiley &amp; Sons, Inc.

Pseudo-prolines in peptide synthesis: Direct insertion of serine and threonine derived oxazolidines in dipeptides

Dipeptides containing serine and threonine derived oxazolidines are prepared by reacting side chain unprotected dipeptides containing C-terminal Thr or Ser with dimethoxypropane. The resulting building blocks can be coupled in Fmoc-based solid phase peptide synthesis enhancing peptide solvation by its secondary structure disrupting potential. The present procedure may be considered as a first step towards a reversible modification of structural and functional properties of bioactive peptides and proteins.

Multiple-buffer-additive strategies for enhanced capillary electrophoretic separation of peptides

A dodeca-peptide from the β-subunit of thyroid stimulating hormone (TSH) was used as a model system for developing “multiple-buffer-additive” strategies to effect the separation of structurally-similar peptides. A series of synthetic peptides included six peptides with identical amino acid composition and two with multiple alanine substitutions at selected positions. Those with identical amino acid composition included the native and reverse sequences of residues 101–112 of the β-TSH and four “computer-shuffled” amino acid sequences. Buffer additives such as acetonitrile (ACN), hexane sulfonic acid (HSA), and hexamethonium bromide (HxMBr), were shown to alter selectivity dramatically. HSA, an ion-pairing agent, and ACN, known to alter the hydrophobic environment of the solute, and HxMBr, which is thought to negate solute-wall interactions, are shown to independently effect only partial resolution of the mixture. It is shown that only with the proper combination of HSA and ACN are all mixture components resolved. These results re-affirm that CE selectivity may be altered by changes in buffer ionic strength or with the addition of HSA, but also show that further changes in selectivity can be achieved through alteration of buffer hydrophobicity. The observed changes in selectivity accompanying the addition of HSA and ACN may be due to differing electrophoretic mobilities resulting from nearest-neighbor effects or subtle differences in peptide secondary structure or solvation. This emphasizes the importance of employing multiple-buffer-additive strategies for effecting the resolution of peptide mixtures that are difficult to separate.

Hydrating peptides using a sprouting technique

AbstractA scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X‐PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley &amp; Sons, Inc.