Partial Molar Volume Change Research Articles

Complex Protein Retention Shifts with a Pressure Increase: An Indication of a Standard Partial Molar Volume Increase during Adsorption?

Studies of protein adsorption on reversed-phase and ion exchange stationary phases demonstrated an increase in retention with increasing pressure, which is interpreted as a standard partial molar volume decrease during the transition of the protein from a mobile to a stationary phase. Investigation of the pressure effect on the retention of lysozyme and IgG on a cation exchange column surprisingly revealed a negative retention trend with the increase of pressure. Further investigation of this phenomenon was performed with β-lactoglobulin, which enabled adsorption to be studied on both cation and anion exchange columns using the same mobile phase with a pH of 5.2. The same surface charge and standard partial molar volume in the mobile phase allowed us to examine only the effect of adsorption. Interestingly, a negative retention trend with a pressure increase occurred on an anion exchange column while a positive trend was present on a cation exchange column. This indicates that the interaction type governs the change in the standard partial molar volume during adsorption, which is independent of the applied pressure. Increasing the protein charge by decreasing the pH of the mobile phase to 4 reversed the retention trend (into a negative) with a pressure increase on the cation exchange column. A further decrease of the pH value resulted in an even more pronounced negative trend. This counterintuitive behavior indicates an increase in the standard partial molar volume during adsorption with the protein charge, possibly due to intermolecular repulsion of adsorbed protein molecules. While a detailed mechanism remains to be elucidated, presented results demonstrate the complexity of ion exchange interactions that can be investigated simply by changing the column pressure.

Harnessing Pressure Modulation for Exploring Ligand Binding Reactions in Cosolvent Solutions

A comprehensive understanding of ligand-protein interactions requires information about all thermodynamic parameters that describe the complexation reaction, and they should be able to provide the necessary information to understand the molecular forces that drive complex formation. Usually, binding studies are performed at ambient pressure conditions. However, in addition to using temperature variation to reveal enthalpic and entropic contributions to ligand binding, complementary pressure-dependent studies providing volumetric properties of the reaction can be beneficial. Changes in partial molar volume can inform about changes in packing and hydration upon ligand binding. Here, after a general discussion of pressure effects on ligand binding reactions, we present a comprehensive study of the effect of pressure and a widely used organic cosolvent, dimethyl sulfoxide (DMSO), on the binding of a small aromatic ligand, proflavine, to the enzyme α-chymotrypsin. We found that DMSO, which acts as a competitive inhibitor for proflavine, has a strong impact on the interaction process, resulting in a decrease of the binding constant. While the reaction performed in neat buffer is basically pressure insensitive, the partial molar volume of the complex in the presence of DMSO is larger compared with the uncomplexed state, rendering the binding constant markedly smaller upon pressurization. We also show that the magnitude and sign of the binding volume provide valuable information about the interaction mechanism and hydration changes, which is of particular interest when cosolvents are present.

水中におけるナフタレン骨格超分子チューブと1,4-ジオキサンの複合体形成と圧力効果

Host-guest interactions between a pair of naphthalene-based molecular tubes (i.e., anti-isomer and syn-isomer) and 1,4-dioxiane have been studied to understand selective recognition. Volume changes for complexation of the amide naphthotubes with 1,4-dioxane were investigated using high-pressure fluorescence and high-pressure NMR spectroscopy. We found that the partial molar volume change (ΔV°) for the association of 1,4-dioxane with the naphthotubes was －6.3±0.1 mL mol－1 for the anti-isomer and 3.2±0.4 mL mol－1 for the syn-isomer. To elucidate the molecular basis of ΔV°, molecular dynamics simulations of the complexation process were also performed. The difference in ΔV° was attributed to variations in the shape and hydration of naphthotube hydrophobic cavities.

Volumetric Properties for the Binding of 1,4-Dioxane to Amide Naphthotubes in Water.

Host-guest interactions between naphthalene-based molecular tubes and small molecules have been studied to understand selective recognition. However, the volumetric properties of complexation remain largely unknown. In this study, we investigated the volumetric properties for the binding of 1,4-dioxane to a pair of naphthotubes (i.e., anti- and syn-isomers), each possessing two inwardly directed amide groups in the hydrophobic cavity, using nuclear magnetic resonance and fluorescence spectroscopy coupled with pressure perturbation. We found that the partial molar volume change for the association of 1,4-dioxane with the naphthotube was -6.3 ± 0.1 mL/mol for the anti-isomer and 3.2 ± 0.4 mL/mol for the syn-isomer. Moreover, the hydrogen bonds of the naphthotubes with 1,4-dioxane were less compressible than those with water molecules, indicating that more rigid hydrogen bonds existed in the complexes with 1,4-dioxane. Molecular dynamics simulations showed that one opening of the cavity in the syn-isomer was widened because of the repulsion between the four COO- charges, which allowed more water molecules to access the hydrophobic cavity than in the case of the anti-isomer. The difference in the partial molar volume change was explained by variations in the hydration of naphthotube hydrophobic cavities. The enhanced understanding of the molecular basis of volume changes during 1,4-dioxane-naphthotube complexation may provide insights into ligand binding to bioreceptors.

Effect of Pressure Increase on Macromolecules' Adsorption in Ion Exchange Chromatography.

In this study a new method for evaluating the pressure effect on separations of oligonucleotides and proteins on an anion exchange column was developed. The pressure rise of up to 500 bar was attained by coupling restriction capillaries to the column outlet to minimize differences in pressure over the column. Using pH transient measurements it was demonstrated that no shift in ion exchange equilibria occurs due to a pressure increase. Results from isocratic and gradient separations of oligonucleotides (model compounds) were evaluated by stoichiometric displacement and linear gradient elution model, respectively. Both elution modes demonstrated that for smaller oligonucleotides the number of binding sites remained unchanged with pressure rise while an increase for large oligonucleotides was observed, indicating their alignment over the stationary phase. From the obtained model parameters and their pressure dependencies, a thermodynamic description was made and compared between the elution modes. A complementary pattern of a linear increase of partial molar volume change with a pressure rise was established. Furthermore, estimation of the pressure effect was performed for bovine serum albumin and thyroglobulin that required gradient separations. Again, a raise in binding site number was found with pressure increase. The partial molar volume changes of BSA and Tg at the maximal investigated pressure and minimal salt concentration were −31.6 and −34.4 cm3/mol, respectively, indicating a higher rigidity of Tg. The proposed approach provides an insight into the molecule deformation over a surface at high pressures under nondenaturing conditions. The information enables a more comprehensive UHPLC method development.

Transition states under pressure

Enzyme Catalysis Enzymes are flexible and dynamic, with conformational changes in the protein, such as movement of a lid over the active site, often limiting the overall rate of turnover. Manipulating pressure offers a means of studying the transition state of processes within which the partial molar volume changes. Using model enzyme variants adapted to high or low pressure, Stiller et al. compared volume and kinetic parameters at pressures up to 50 megapascals. The piezophilic enzyme showed pressure-dependent activity resulting from hydration of the active site early in the lid-opening process. Three point mutations that disrupt a network of salt bridges that form during lid-opening can confer pressure sensitivity on the mesophilic enzyme, presumably by changing the hydration of the active site at the transition state. Nat. Catal. 10.1038/s41929-019-0307-6 (2019).

H2O–CO2 solubility in alkali-rich mafic magmas: new experiments at mid-crustal pressures

Volatile solubility in magmas depends on several factors, including composition and pressure. Mafic magmas with high concentrations of alkali elements are capable of dissolving larger quantities of H2O and CO2 than subalkaline basalt, which possibly contributes to large explosive eruptions. Existing volatile solubility models for alkali-rich mafic magmas are well calibrated below ~ 200 MPa, but at greater pressures the experimental data are sparse. To fill in this gap, we conducted a set of mixed H2O–CO2 volatile solubility experiments between 400 and 600 MPa at 1200 °C in six mafic compositions with variable alkali contents (Stromboli, Etna, Vesuvius, Erebus, Sunset Crater, and the San Francisco Volcanic Field). Results from our experiments indicate that existing volatile solubility models for alkali-rich mafic magmas, if extrapolated beyond their calibrated ranges, do not accurately describe CO2 solubility at mid-crustal pressures. We adapt an existing thermodynamic model to reflect our higher-pressure experimental data by determining model parameters $$\Delta {\text{V}}_{r}^{0,m}$$ (partial molar volume change of CO2 reaction) and K0 (equilibrium constant) for each studied composition. In these compositions, $$\Delta {\text{V}}_{r}^{0,m}$$ is found to vary between ~ 15 and ~ 25 cm3 mol−1, while ln K0 ranges from − 14.9 to − 14.0. The calculated solubility curves show good agreement with CO2 solubility data from the experiments and provide a more accurate description of CO2 solubility than purely empirical fits. These new experiments indicate while CO2 solubility is increased in alkali-rich mafic magmas, it is not simply controlled by total alkali content but rather the full multicomponent magma composition.

Time-Resolved Study of Interprotein Signaling Process of a Blue Light Sensor PapB-PapA Complex.

PapB is a short BLUF protein from the purple bacterium Rhodopseudomonas palustris, and it has the function of regulating the phosphodiesterase activity of its partner protein PapA. Because PapA is an enzymatic protein containing an EAL domain, which hydrolyzes a cyclic-dimeric-GMP, the PapB-PapA complex regulates, for example, biofilm formation in a light-dependent manner. The reaction dynamics of PapB, as well as dynamics of signal transduction in the PapB-PapA complex, were studied mostly by time-resolved transient grating and CD methods. It was found that although PapB exists as a monomer in both dark and light states, the diffusion coefficient slightly increases and partial molar volume changes upon light irradiation with time constants of 80 μs, 3.2 ms, and 24 ms. The last conformational change leads to a signaling state that is attributed to the α-helix unfolding in the C-terminal region of the BLUF domain. Interestingly, when PapA is added to a PapB solution to form a PapB-PapA complex, the diffusion coefficient decreases significantly, with a time constant of 26 ms, which is similar to the rate of the last conformational change of PapB. It was found that this change is due to the conformational change of PapA, and the light signal from PapB is transmitted through the conformational change of PapB. Compared with another BLUF protein, BlrP1, which possesses the EAL effector domain and requires photoexcitation of two monomer units of the dimer for a major conformational change, the conformational change of the PapB-PapA complex is induced by excitation of one monomer PapB among the heterotetramer.

Uncovering dehydration in cytochrome <i>c</i> refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy

To investigate the dehydration associated with protein folding, the partial molar volume changes for protein unfolding (ΔVu) in cytochrome c (Cyt c) were determined using high pressure absorption spectroscopy. ΔVu values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56±5 and 29±1 mL mol−1, respectively. Considering that the volume change for hydration of hydrophobic groups is positive and that Cyt c has a covalently bonded heme, a positive ΔVu reflects the primary contribution of the hydration of heme. Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive ΔVu. On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. To unfold such partial structures, we introduced a mutation near the heme binding site, His26, to Gln, resulting in a negatively shifted ΔVu (4±2 mL mol−1) in urea-denatured Cyt c. The formation of the more solvated and less structured state in the urea-denatured mutant enhanced hydration to the hydrophilic groups in the unfolding process. Therefore, we confirmed the hydration of amino acid residues in the protein unfolding of Cyt c by estimating ΔVu, which allows us to discuss the hydrated structures in the denatured states of proteins.

Lysozyme Stabilization under High Pressure: Differential Scanning Microcalorimetry

The heat denaturation of lysozyme has been studied by high-pressure differential scanning microcalorimetry. It has been demonstrated that an increase in pressure has different influence on denaturation temperature and enthalpy at different pH values. It has been established that the pressure increase has no appreciable effect on the transition cooperativity. The experimental data have been analyzed using an equilibrium model of transition between two states. Partial molar volume changes accompanying the denaturation as well as isothermal compressibility and thermal expansibility coefficients have been assessed. In contrast to the denaturation of most globular proteins, the lysozyme denaturation under conditions of the experiment was accompanied by positive volume changes. Possible reasons for this unusual behavior have been discussed.

Thermodynamics of aqueous adenine: Standard partial molar volumes and heat capacities of adenine, adeninium chloride, and sodium adeninate from T = 283.15 K to 363.15 K

Apparent molar volumes, Vϕ, and apparent molar heat capacities, Cp,ϕ, were measured for aqueous solutions of neutral adenine (AdH) and adeninium chloride (AdH2Cl) at temperatures from 288.15K to 363.15K, and for sodium adeninate (NaAd) at temperatures from 283.15K to 313.15K. Density measurements used in the determination of the standard partial molar volume, Vo, were made with a vibrating-tube densimeter at ambient pressure. Heat capacity measurements used in the determination of the standard partial molar heat capacity, Cpo, were made with a twin fixed-cell, differential output, power compensating, temperature-scanning calorimeter at a pressure of 0.4MPa. The contributions from minor equilibrium species were removed using Young’s Rule to yield values for the standard partial molar volume and heat capacities of the ionic species AdH2+(aq) and Ad−(aq), and the equilibrium mixture of neutral species AdH∗(aq). Semi-empirical equations describing the temperature dependence of Vo and Cpo for each species were fitted by regression to the experimental results. From these equations, the standard partial molar volume change ΔrVom and heat capacity change ΔrCpom for the ionization reactions were calculated. The standard partial molar volumes presented in this study for neutral adenine are the first to be experimentally determined at temperatures above 330K, while the standard partial molar heat capacities are the first to be reported at temperatures above 298.15K. The experimental values for the adeninium cation and adeninate anion are the first to be reported in the literature.

Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr, of TBA with a mutation from T to A in the 5′ most loop (TBA T3A) was 75.5cm3mol−1, which was larger than that of TBA (54.6cm3mol−1). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆Vtr of 41.1cm3mol−1. In the presence of poly(ethylene)glycol 200 (PEG200), ∆Vtr values were 14.7cm3mol−1 for TBA T3A and 13.2cm3mol−1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures.

Pressure Effect on the Folding of G-Quadruplex DNA Modified with Hexaethylene Glycol

Objective: Pressure can influence the folding of nucleic acids, and the effect of pressure depends on the volumetric difference between folded and unfolded states. In this study, we investigated how modification with hexaethylene glycol affected the folding of a guanine-rich DNA oligonucleotide. Results: The stability of the G-quadruplex formed by the thrombin binding aptamer (TBA), 5’-GGTTGGTGTGGTTGG-3’ (loop regions underlined) modified with hexaethylene glycol (HEG) at the 5’-terminus decreased more significantly as pressure increased than did the G-quadruplex formed by the unmodified TBA. The change of partial molar volume, ΔV, of 5-HEG TBA folding was 101 cm3 mol-1, where as that of TBA was 54.6 cm3 mol-1. The HEG at 5’ terminus of TBA increased volume of the folded structure due to induction of dehydration. In contrast, replacement of the 5’-most loop of the TBA G-quadruplex with HEG resulted in a ΔV value of 62.8 cm3 mol-1, whereas replacement of the second loop resulted in a ΔV value of 82.8 cm3 mol-1. It has been suggested that bases of the nucleotides in the second loop form stacking interaction with G-quartet but those in the first loop do not. Conclusion: These results indicate that a 5’ covalently linked HEG disrupts the stacked structure of the second loop on the G-quartet; this stacking accompanied dehydration during the quadruplex formation. Thus, modification with poly(ethylene glycol) units enhances the effect of pressure on the folding of G-quadruplex DNA.

Osmotic Pressure Effects Reveal a Specific Dehydration-Induced Hydrophobic Electron Transfer Structure Comprising Cytochrome C and Cytochrome C Oxidase

In the mitochondrial respiratory chain, Cytochrome c oxidase (CcO) accepts electrons from Cytochrome c (Cyt c) to reduce molecular oxygen. Previous studies showed that the complex formation of Cyt c with CcO is characterized by the positive entropy change, suggesting the dehydration from hydrophobic residues, but no experimental evidence of such dehydration has been reported. To confirm the dehydration during the complex formation between Cyt c and CcO, we focused on the partial molar volume change of protein (ΔV W) for the complex formation, which reflects the volume of dehydrated water molecules. ΔV W is correlated with the osmotic pressure (π) dependence of the K d. Osmotic pressure was increased by addition of sugars or polyols having no specific interactions with proteins and K d was estimated by the Michaelis-Menten analysis of the steady state kinetics for the electron transfer from Cyt c to CcO. As Figure 1 shows, the K d value is decreased with increasing the osmotic pressure, corresponding to the negative ΔV W of – 300 ± 78 mL mol-1. Assuming that the partial molar volume change of one hydrated water molecule around hydrophobic residues would be－17.5 mL mol-1, the volume change we obtained here corresponds to the dehydration of 17 ± 4 water molecules. Considering that the entropy change from the dehydration (dehydΔS) of one water molecule was estimated to be 5.5 JK-1mol-1, dehydΔS of 17 water molecules corresponds to ~90 JK-1mol-1, which is about 75% of total entropy change for the Cyt c-CcO complex formation. The dehydration is, therefore, one of the major factors to increase the entropy for the complex formation. To identify the dehydration sites from hydrophobic residues in the interaction site for CcO on Cyt c, we mutated Ile11 or Ile81, hydrophobic amino acid residues in the interaction site for CcO [1], to Ala, an amino acid residue having a smaller side chain and less number of the hydrated water molecules. As clearly illustrated in Figure 1, the slope of the osmotic pressure dependence of K d for the Ile mutant is less steep than that for the wild type protein. The estimated numbers of the dehydrated water molecules were reduced to 13 ± 3 and 8 ± 2 for the Ile11 and Ile81 mutants, respectively. The reduced numbers of the dehydrated water molecules in these Ile mutants indicate that the hydrated water molecules around Ile11 and Ile81 were expelled to the solvent in the complex formation between Cyt c and CcO. In conclusion, we successfully identified that about 17 water molecules are dehydrated in the Cyt c-CcO complex formation and the primary dehydration sites are Ile11 and Ile81. Such dehydration from the hydrophobic residues can be a major factor to increase the entropy, facilitating the complex formation and the electron transfer from Cyt c to CcO.

Negative thermal expansibility change for dissociation of lysozyme variant amyloid protofibril.

A disulfide-deficient variant of hen lysozyme, 0SS, is known to form an amyloid protofibril spontaneously, and to dissociate into monomers at high hydrostatic pressure. We carried out native PAGE at various temperatures (20-35°C) and pressures (0.1-200 MPa), to characterize the dissociation equilibrium of disulfide-deficient variant of hen lysozyme amyloid protofibril. Based on the density profiles, the partial molar volume and thermal expansibility changes for dissociation, ΔvD and ΔeD , were obtained to be -74 cm(3) /mol at 25°C and -2.3 cm(3) mol(-1) K(-1) , respectively. The dissociation of amyloid fibril destroys the cross β-structure, and such conformational destruction in native protein fold rarely accompanies negative thermal expansibility change. We discussed the negative thermal expansibility change in terms of hydration and structural packing of the amyloid protofibril.

Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide

While most proteins unfold under high-pressure conditions, some high-pressure experiments suggest that an AK16 peptide forms more helical structures. In order to understand this abnormality, molecular dynamics simulations with the simulated tempering method for the isobaric–isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. It was found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behaviour under high-pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure. Moreover, interatomic distances of AK16 become shorter at high pressure than at low pressure. These behaviours indicate that the helical structures are squeezed by high pressure.

Molecular dynamics of the structural changes of helical peptides induced by pressure.

An AK16 peptide and a C-peptide analog are experimentally known to form more helical structures under high-pressure conditions than those at atmospheric pressure, even though most proteins usually unfold at high pressure. To understand the pressure-induced structural changes of the two peptides, molecular dynamics simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. We found that the fraction of the folded state decreases once and then increases with increasing pressure for both peptides. The partial molar volume change of both peptides from the folded state to the unfolded state increases monotonically from a negative value to a positive value as pressure increases. By calculating the radius of gyration and interatomic distances of the AK16 peptide and the C-peptide analog, we found that these peptides are compressed under high-pressure conditions, which causes the folded state to be more stable at high pressure. Furthermore, we found that the salt bridge of the C-peptide analog is broken under high pressure.

Temperature and pressure based NMR studies of detergent micelle phase equilibria.

Bulk thermodynamic and volumetric parameters (ΔGmic°, ΔHmic°, ΔSmic°, ΔCp,mic°, ΔVmic°, and Δκmic°) associated with the monomer–micelle equilibrium, were directly determined for a variety of common detergents [sodium n-dodecyl sulfate (SDS), n-dodecyl phosphocholine (DPC), n-dodecyl-β-d-maltoside (DDM), and 7-cyclohexyl-1-heptyl phosphocholine (CyF)] via 1H NMR spectroscopy. For each temperature and pressure point, the critical micelle concentration (cmc) was obtained from a single 1H NMR spectrum at a single intermediate concentration by referencing the observed chemical shift to those of pure monomer and pure micellar phases. This permitted rapid measurements of the cmc over a range of temperatures and pressures. In all cases, micelle formation was strongly entropically favored, while enthalpy changes were all positive, with the exception of SDS, which exhibited a modestly negative enthalpy of micellization. Heat capacity changes were also characteristically negative, while partial molar volume changes were uniformly positive, as expected for an aggregation process dictated by hydrophobic effects. Isothermal compressibility changes were found to be consistent with previous measurements using other techniques. Thermodynamic measurements were also related to spectroscopic studies of topology and micelle structure. For example, paramagnetic effects resulting from the addition of dioxygen provided microscopic topological details concerning the hydrophobicity gradient along the detergent chains within their respective micelles as detected by 1H NMR. In a second example, combined 13C and 1H NMR chemical shift changes arising from application of high pressure, or upon micellization, of CyF provided site-specific details regarding micelle topology. In this fashion, bulk thermodynamics could be related to microscopic topological details within the detergent micelle.

High Pressure Effect on a Helical Peptide Studied by Simulated Tempering Molecular Dynamics Simulations

High pressure effect on proteins and peptides has recently been studied theoretically and experimentally to understand structural properties of proteins such as protein folding and the function of proteins. While some proteins are denatured under high pressure conditions, some peptides are more stable at high pressure than at atmospheric pressure. It is important to understand the molecular mechanism of pressure-induced structural changes of proteins and peptides.We studied pressure effect on the structure of a helical peptide by using molecular dynamics simulations. We used an AK16 peptide as a helical peptide. AK16 is more helical under high pressure conditions than at atmospheric pressure. Molecular simulations often get trapped in the local minimum states of the free energy. In order to overcome such difficulty, we used a generalized-ensemble algorithm, which gives more efficient sampling in a molecular simulation. The simulated tempering method for the isobaric-isothermal ensemble (Y. Mori and Y. Okamoto, JPSJ 79, 074003, 2010) was used for efficient sampling in pressure space.We performed molecular dynamics simulations with the simulated tempering method for the system of AK16 in explicit water molecules. We found that the population of the helical structure of the peptide increases as pressure increases. We also calculated the free energy difference and the partial molar volume change as a function of pressure. The partial molar volume change from the helical state to the coil state increased monotonically from a negative value to a positive value with pressure. The positive value of the partial molar volume change is consistent with experimental results. We revealed the molecular details of AK16 under high pressure conditions (Y. Mori and H. Okumura, JPCL 4, 2079, 2013).

Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations

It is known experimentally that an AK16 peptide forms more α-helix structures with increasing pressure while proteins unfold in general. In order to understand this abnormality, molecular dynamics (MD) simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 1.0 × 10(-4) GPa to 1.4 GPa. From the results of the simulations, it is found that the fraction of the folded state decreases once and increases after that with increasing pressure. The partial molar volume change from the folded state to unfolded state increases monotonically from a negative value to a positive value with pressure. The behavior under high pressure conditions is consistent with the experimental results. The radius of gyration of highly helical structures decreases with increasing pressure, which indicates that the helix structure shrinks with pressure. This is the reason why the fraction of the folded state increases as pressure increases.