Distribution of Helicity within the Model Peptide Acetyl(AAQAA)3amide

Shalongo, William; Dugad, L. B.; Stellwagen, Earle

doi:10.1021/ja00097a039

Cited by 121 publications

(219 citation statements)

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“…1. The approach is then verified by folding simulations of a synthetic peptide with the sequence of (AAQAA) 3 and a small peptide from residues 101-111 of a-lactalbumin (a-lac) whose conformational equilibria have been determined previously (Demarest et al, 1999;Shalongo et al, 1994). We note that these efforts represent only preliminary steps in the development of a fully consistent implicit (GB) solvent force field, but the present studies illustrate the general approach one should use in developing such a force field.…”

Section: A Influence Of Backbone H-bond Strength On Conformational Ementioning

confidence: 80%

Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models

Chen

Brooks

2005

Advances in Protein Chemistry

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Section: A Influence Of Backbone H-bond Strength On Conformational Ementioning

confidence: 80%

Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models

Chen

Brooks

2005

Advances in Protein Chemistry

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“…This allows us to test specifically the effects of the water model using closely related protein force fields that have very similar helical populations under standard conditions of temperature and pressure. We study the 15-residue peptide Ac-(AAQAA) 3 -NH 2 , as a model system which is known to form helix at low temperature, 29 and which has been extensively characterized in previous simulations. 19,21,30 REMD simulations were performed in order to sample the temperature-dependent helix-coil equilibrium.…”

Section: Resultsmentioning

confidence: 99%

Role of solvation in pressure-induced helix stabilization

Best

Miller

Mittal

2014

The Journal of Chemical Physics

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In contrast to the well-known destabilization of globular proteins by high pressure, recent work has shown that pressure stabilizes the formation of isolated α-helices. However, all simulations to date have obtained a qualitatively opposite result within the experimental pressure range. We show that using a protein force field (Amber03w) parametrized in conjunction with an accurate water model (TIP4P/2005) recovers the correct pressure-dependence and an overall stability diagram for helix formation similar to that from experiment; on the other hand, we confirm that using TIP3P water results in a very weak pressure destabilization of helices. By carefully analyzing the contributing factors, we show that this is not merely a consequence of different peptide conformations sampled using TIP3P. Rather, there is a critical role for the solvent itself in determining the dependence of total system volume (peptide and solvent) on helix content. Helical peptide structures exclude a smaller volume to water, relative to non-helical structures with both the water models, but the total system volume for helical conformations is higher than non-helical conformations with TIP3P water at low to intermediate pressures, in contrast to TIP4P/2005 water. Our results further emphasize the importance of using an accurate water model to study protein folding under conditions away from standard temperature and pressure.

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“…In the CD investigations reported here, there is no indication that A3 or B6 shows a similar conversion to β-sheet; their temperature-dependent conformational behavior is similar to that of other previously reported alanine-rich peptides. 23,24,57,58 The thermal stability of the protein polymers at higher concentrations of 1 mg/mL in pH 2.3, 10 mM phosphate buffer was also monitored via differential scanning calorimetry. Figure 3a shows the calorimetric data for both A3 and B6 at a scan rate of 60 °C/h.…”

Section: Resultsmentioning

confidence: 99%

Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups

et al. 2005

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Protein engineering strategies have proven valuable for the production of a variety of well-defined macromolecular materials with controlled properties that have enabled their use in a range of materials and biological applications. In this work, such biosynthetic strategies have been employed in the production of monodisperse alanine-rich, helical protein polymers with the sequences [AAAQEAAAAQAAAQAEAAQAAQ] 3 and [AAAQAAQAQAAAEAAAQAAQAQ] 6 . The composition of these protein polymers is similar to that of a previously reported family of alaninerich protein polymers, but the density and placement of chemically reactive residues has been varied to facilitate the future use of these macromolecules in elucidating polymeric structure-function relationships in biological recognition events. Both protein polymers are readily expressed from E. coli and purified to homogeneity; characterization of their conformational behavior via circular dichroic spectroscopy (CD) indicates that they adopt highly helical conformations under a range of solution conditions. Differential scanning calorimetry, in concert with CD, demonstrates that the conformational transition from helix to coil in these macromolecules can be well-defined, with helicity, conformational transitions, T m values, and calorimetric enthalpies that vary with the molecular weight of the protein polymers. A combination of infrared spectroscopy and CD also reveals that the macromolecules can adopt β-sheet structures at elevated temperatures and concentrations and that the existence and kinetics of this conformational transition appear to be related to the density of charged groups on the protein polymer.

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Distribution of Helicity within the Model Peptide Acetyl(AAQAA)3amide

Cited by 121 publications

References 0 publications

Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models

Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models

Role of solvation in pressure-induced helix stabilization

Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups

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