General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly
<p>Schematic representation of three side chains. The excluded volume generated by a side chain is the volume occupied by the side chain itself plus the volume shown in gray. When side chains are closely packed, the excluded volumes overlap, leading to a gain of the water entropy.</p> "> Figure 2
<p>Reduced density profiles of hard-sphere solvent near a hard-sphere solute <span class="html-italic">g</span><sub>US</sub>(<span class="html-italic">r</span>) at <span class="html-italic">ρ</span><sub>S</sub><span class="html-italic">d</span><sub>S</sub><sup>3</sup> = 0.2 (dotted line), <span class="html-italic">ρ</span><sub>S</sub><span class="html-italic">d</span><sub>S</sub><sup>3</sup> = 0.5 (2-dot dashed line), and <span class="html-italic">ρ</span><sub>S</sub><span class="html-italic">d</span><sub>S</sub><sup>3</sup> = 0.7 (solid line).</p> "> Figure 3
<p>(a) <span class="html-italic">C</span><sub>1</sub> (Å<sup>−3</sup>), <span class="html-italic">C</span><sub>2</sub> (Å<sup>−2</sup>), and <span class="html-italic">C</span><sub>2</sub>/<span class="html-italic">C</span><sub>1</sub> (Å) of solvation entropy, −<span class="html-italic">S</span>/k<sub>B</sub>, plotted against solvent density corresponding to the pressure. (b) <span class="html-italic">C</span><sub>1</sub> and <span class="html-italic">C</span><sub>2</sub> (Å) of partial molar volume plotted against solvent density.</p> "> Figure 4
<p>Negative of the entropy change of solvent scaled by k<sub>B</sub> upon the transition from the native structure to (a) the swelling structure and (b) the random-coil structures of protein G plotted against the bulk solvent density corresponding to the pressure <span class="html-italic">P</span>. −Δ<span class="html-italic">S</span>/k<sub>B</sub> = (−<span class="html-italic">S</span>/k<sub>B</sub>)<sup>Unfold</sup>−{(−<span class="html-italic">S</span>/k<sub>B</sub>)<sup>Native</sup>} where the superscripts “Native” and “Unfold” represent the values for the native structure and for the unfolded structure, respectively. (c) Decomposition of −Δ<span class="html-italic">S</span>/k<sub>B</sub> for swelling structure of protein G [<a href="#entropy-12-01632-f004" class="html-fig">Figure 4</a>(a)] into <span class="html-italic">C</span><sub>1</sub>Δ<span class="html-italic">V</span><sub>ex</sub>, <span class="html-italic">C</span><sub>2</sub>Δ<span class="html-italic">A</span>, and <span class="html-italic">C</span><sub>3</sub>Δ<span class="html-italic">X</span>+<span class="html-italic">C</span><sub>4</sub>Δ<span class="html-italic">Y</span> at each bulk solvent density.</p> "> Figure 5
<p>Δ<span class="html-italic">S</span> and |Δ<span class="html-italic">S</span><sub>C</sub>| plotted against the bulk solvent density corresponding to the pressure. |Δ<span class="html-italic">S</span><sub>C</sub>| lies between the two dashed lines. The SE gain and the CE loss upon the transition from the coil state (an ensemble of random coils) to the complete α-helix structure are compared.</p> ">
Abstract
:1. Introduction
2. Driving Force of Pressure Denaturation of Proteins: Translational Entropy of Water
EV (Å 3) | ASA (Å 2) | |
---|---|---|
Native | 11,600.3 | 3,670.90 |
Swelling | 11,926.9 | 4,210.81 |
Random coil | 14,002.9 | 5,947.13 |
3. Models and Theoretical Approach for the Calculation of Solvation Thermodynamic Quantities
3.1. Models
3.2. Morphometric Approach
3.3. Quantitative Comparison between Experimental and Theoretical Results for Apoplastocyanin Folding
4. General Framework of Pressure Effects on Structures Formed by Self-assembly
4.1. Microscopic Mechanism of Pressure Denaturation of Proteins
4.2. Pressure-induced Helix-coil Transition of a Polypeptide
4.3. Comment on Formation/Dissociation Process of Amyloid Fibrils
5. Conclusions
Acknowledgements
References and Notes
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Yoshidome, T. General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly. Entropy 2010, 12, 1632-1652. https://doi.org/10.3390/e12061632
Yoshidome T. General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly. Entropy. 2010; 12(6):1632-1652. https://doi.org/10.3390/e12061632
Chicago/Turabian StyleYoshidome, Takashi. 2010. "General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly" Entropy 12, no. 6: 1632-1652. https://doi.org/10.3390/e12061632