A Molecular Dynamics and Quantum Mechanics Analysis of the Effect of DMSO on Enzyme Structure and Dynamics: Subtilisin

Stability of angiogenic agents, ginsenoside Rg1 and Re, isolated from Panax ginseng: In vitro and in vivo studies

The study was designed to investigate the stability of ginsenoside Rg(1) (Rg(1)) and Re (Re), two natural herbal compounds isolated from Panax ginseng, based on their activity to promote angiogenesis in vitro and in vivo. After being treated at different temperatures, pHs, and solvent species for distinct durations, the remaining activities of Rg(1) and Re on human umbilical vein endothelial cell (HUVEC) proliferation, migration, and tube formation were examined in vitro. Additionally, the remaining activity of each treated test agent, mixed in a growth factor-reduced Matrigel, in stimulating angiogenesis was evaluated subcutaneously in a mouse model. Basic fibroblast growth factor (bFGF) was used as a control. It was found in vitro that HUVEC proliferation, migration in a Transwell plate, and tube formation on Matrigel were all significantly enhanced in the presence of bFGF, Rg(1), or Re. However, after being treated at different temperatures, pHs, or solvent species, the remaining activity of bFGF on HUVEC behaviors reduced significantly. This observation was more significant with increasing the duration of treatment. In contrast, the activities of Rg(1) and Re remained unchanged throughout the entire course of the study. The in vivo results observed on day 7 after implantation showed that the blank control (Matrigel alone) was slightly vascularized. In contrast, the density of neo-vessels in the Matrigel plug mixed with bFGF, Rg(1), or Re was significantly enhanced. However, after being treated, the density of neo-vessels was significantly reduced in the Matrigel plug mixed with bFGF, while those of Rg(1) and Re remained unchanged. The aforementioned results suggested that Rg(1) and Re could be a novel group of nonpeptide angiogenic agents with a superior stability and may be used for the management of tissue regeneration.

Molecular-dynamics simulations of dimethylsulfoxide-methanol mixtures

We present molecular-dynamics (MD) computer simulation results for the local structures, hydrogen (H)-bond distribution, and dynamical properties of methanol (MeOH) and dimethylsulfoxide (DMSO) binary mixtures at ambient conditions over the entire composition range. The simulated heat of mixing and site-site pair distribution functions suggest that the intermolecular structures of the pure liquids are not markedly altered upon mixing. Nevertheless, H-bonding statistics show that aggregates of the type 1DMSO:1MeOH are formed and represent the predominant form of molecular association in these mixtures. Only a small fraction (10%) of DMSO molecules in MeOH-rich mixtures (85% in mole) forms H-bonding trimers of type 1DMSO:2MeOH. No evidence of other types of interspecies association is found. The self-diffusion coefficient for DMSO (MeOH) increases (decreases) upon mixing. The characteristic reorientation time tau1 of both species increases in the mixture, but the composition dependence is weak. The frequency spectrum of MeOH reorientational time-correlation function shows significant redshifts of the principal librational band as DMSO is added to the system, whereas the librational band of DMSO shows small alterations upon mixing. Our results are discussed in the light of previous simulation analyses for a similar system, DMSO-water mixtures, and compared with available experimental results.

Chiral recognition by mass-resolved laser spectroscopy

Chiral recognition is a fundamental phenomenon in life sciences, based on the enantioselective complexation of a chiral molecule with a chiral selector. The diastereomeric aggregates, formed by complexation, are held together by a different combination of intermolecular forces and are therefore endowed with different stability and reactivity. Determination of these forces, which are normally affected in the condensed phase by solvent and supramolecular interactions, requires the generation of the diastereomeric complexes in the isolated state and their spectroscopic investigation. This review deals with chiral recognition in the gas phase through the application of laser-resolved mass spectrometric techniques (R2PI-TOF and RET-MS). The measurement of the fragmentation thresholds of diastereomeric clusters by these techniques allows the determination of the nature of the intrinsic interactions, which control their formation and affect their stability and reactivity.

Molecular dynamics simulations of acetonitrile/dimethyl sulfoxide liquid mixtures

Binary liquid mixtures of dimethyl sulfoxide and acetonitrile at the three molar fractions 0.25, 0.50, and 0.75 have been investigated by molecular dynamics computer simulations. Thermodynamic states corresponding to liquid-vapor coexistence at a temperature of 298 K were considered. Intermolecular interactions were described by potential models of the site-site (12-6) Lennard-Jones plus Coulomb type that have been developed for the description of the pure liquids. Dimethyl sulfoxide has been represented by four interactions sites and acetonitrile by a three- as well as a six-site potential model. We have calculated thermodynamic properties and the intermolecular pair distribution functions. Intermolecular interaction energies indicate deviations from the behavior of ideal mixtures. The local mole fraction analysis demonstrates that dimethyl sulfoxide is preferentially solvated by acetonitrile and that the first solvation shell surrounding acetonitrile molecules is significantly enriched by dimethyl sulfoxide. The nonideal behavior in the mixtures is not affected by the choice of the three- or the six-site potential model for acetonitrile. Orientational correlations of dipole vectors within the first solvation shells indicate that the relative molecular orientations found in pure acetonitrile and dimethyl sulfoxide are maintained in the mixtures. Parallel and antiparallel dipole-dipole configurations determine first shell acetonitrile-dimethyl sulfoxide configurations. Dynamical features of the mixtures are discussed in terms of diffusion constants and orientational correlation times as obtained from the time correlation functions for linear velocities and molecular dipole moments, respectively. Computed relaxation times indicate faster reorientational motion for dimethyl sulfoxide if acetonitrile is added. In contrast, the orientational dynamics of acetonitrile becomes stronger correlated upon dilution with dimethyl sulfoxide. The diffusion coefficients for both compounds follow this tendency.

Is the C-terminal Region of Bradykinin the Binding Site of Polyphenols?

Bradykinin is a bioactive hormone involved in a variety of physiological processes. In various solvents, this peptide adopts beta-turn structures. The C-terminal turn is a structural feature for the receptor affinity of agonists and antagonists while the N-terminal turn might be important for antagonistic activities. Polyphenols like dimeric proanthocyanidin B3 interact with the peptide. Thus to investigate the effects of polyphenols on bradykinin activity and structure, we studied the interaction in the structuring solvent DMSO which can be a close mimic of aqueous physiological environments like receptor-binding sites. Bradykinin alone presented a folded structure with two turns. B3 interacted with the peptide C-terminus and involved the loss of the bend structure of this region, while the N-terminus turn was maintained. Numerous studies have shown that polyphenolic molecules can act upon various biological targets, and the formation of this type of complex might be one of the possible modes of action.

Water-miscible organic cosolvents enhance phosphatidylinositol-specific phospholipase C phosphotransferase as well as phosphodiesterase activity

Phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis catalyzes the hydrolysis of phosphatidylinositol (PI) in a Ca(2+)-independent two-step mechanism: (i) an intramolecular phosphotransferase reaction to form inositol 1,2-(cyclic)-phosphate (cIP), followed by (ii) a cyclic phosphodiesterase activity that converts cIP to inositol 1-phosphate (I-1-P). Moderate amounts of water-miscible organic solvents have previously been shown to dramatically enhance the cyclic phosphodiesterase activity, that is, hydrolysis of cIP. Cosolvents [isopropanol (iPrOH), dimethylsufoxide (DMSO), and dimethylformamide (DMF)] also enhance the phosphotransferase activity of PI-PLC toward PI initially presented in vesicles, monomers, or micelles. Although these water-miscible organic cosolvents caused large changes in PI particle size and distribution (monitored with pyrene-labeled PI fluorescence, 31P NMR spectroscopy, gel filtration, and electron microscopy) that differed with the activating solvent, the change in PI substrate structure in different cosolvents was not correlated with the enhanced catalytic efficiency of PI-PLC toward its substrates. PI-PLC stability was decreased in water/organic cosolvent mixtures (e.g., the T(m) for PI-PLC thermal denaturation decreased linearly with added iPrOH). However, the addition of myo-inositol, a water-soluble inhibitor of PI-PLC, helped stabilize the protein. At 30% iPrOH and 4 degrees C (well below the T(m) for PI-PLC in the presence of iPrOH), cosolvent-induced changes in protein secondary structure were minimal. iPrOH and diheptanoylphosphatidylcholine, each of which activates PI-PLC for cIP hydrolysis, exhibited a synergistic effect for cIP hydrolysis that was not observed with PI as substrate. This behavior is consistent with a mechanism for cosolvent activation that involves changes in active site polarity along with small conformational changes involving the barrel rim tryptophan side chains that have little effect on protein secondary structure.

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.

Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies

Protein structure and dynamics in nonaqueous solvents are here investigated using molecular dynamics simulation studies, by considering two model proteins (ubiquitin and cutinase) in hexane, under varying hydration conditions. Ionization of the protein groups is treated assuming "pH memory," i.e., using the ionization states characteristic of aqueous solution. Neutralization of charged groups by counterions is done by considering a counterion for each charged group that cannot be made neutral by establishing a salt bridge with another charged group; this treatment is more physically reasonable for the nonaqueous situation, contrasting with the usual procedures. Our studies show that hydration has a profound effect on protein stability and flexibility in nonaqueous solvents. The structure becomes more nativelike with increasing values of hydration, up to a certain point, when further increases render it unstable and unfolding starts to occur. There is an optimal amount of water, approximately 10% (w/w), where the protein structure and flexibility are closer to the ones found in aqueous solution. This behavior can explain the experimentally known bell-shaped dependence of enzyme catalysis on hydration, and the molecular reasons for it are examined here. Water and counterions play a fundamental and dynamic role on protein stabilization, but they also seem to be important for protein unfolding at high percentages of bound water.

Molecular dynamics simulation of DPPC bilayer in DMSO

We performed molecular dynamics simulations on dipalmitoylphosphatidylcholine (DPPC)/dimethylsulfoxide (DMSO) system that has the same lipid:solvent weight ratio as in our previous simulation done on DPPC/water. We did not observe a large change in the size of DPPC membrane when the solvent was changed from water to DMSO. Also, we did not observe that a large number of DMSO molecules is permeating into the membrane, as it was suggested to explain the observed change in the bilayer repeat period. We found that the surface potential reverses its sign when water is replaced by DMSO. Based on the results from our simulations, we propose that the repulsion force acting between membranes is reduced when DMSO is added to solvent water and therefore membrane surfaces approach closer to each other and the extra solvent is removed into excess solution.

Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water

The x-ray crystal structures of trans-cinnamoyl-subtilisin, an acyl-enzyme covalent intermediate of the serine protease subtilisin Carlsberg, have been determined to 2.2-A resolution in anhydrous acetonitrile and in water. The cinnamoyl-subtilisin structures are virtually identical in the two solvents. In addition, their enzyme portions are nearly indistinguishable from previously determined structures of the free enzyme in acetonitrile and in water; thus, acylation in either aqueous or nonaqueous solvent causes no appreciable conformational changes. However, the locations of bound solvent molecules in the active site of the acyl- and free enzyme forms in acetonitrile and in water are distinct. Such differences in the active site solvation may contribute to the observed variations in enzymatic activities. On prolonged exposure to organic solvent or removal of interstitial solvent from the crystal lattice, the channels within enzyme crystals are shown to collapse, leading to a drop in the number of active sites accessible to the substrate. The mechanistic and preparative implications of our findings for enzymatic catalysis in organic solvents are discussed.

Solvent influence on base stacking

In this paper we present a detailed analysis of the base-stacking phenomenon in different solvents, using nanosecond molecular dynamics simulations. The investigation focuses on deoxyribo- and ribodinucleoside monophosphates in aqueous and organic solutions. Organic solvents with a low dielectric constant, such as chloroform, and solvents with intermediate dielectric constants, such as dimethyl sulfoxide and methanol, were analyzed. This was also done for water, which is highly polar and has a high dielectric constant. Structural parameters such as the sugar puckering and the base-versus-base orientations, as well as the energetics of the solute-solvent interactions, were examined in the different solvents. The obtained data demonstrate that base stacking is favored in the high dielectric aqueous solution, followed by methanol and dimethyl sulfoxide with intermediate dielectric constants, and chloroform, with a low dielectric constant.

The interactions with solvent, heat stability, and 13C-labelling of alamethicin, an ion-channel-forming peptide

The peptide alamethicin was labelled with 13C and 15N by growing the fungus Trichoderma viride in a medium containing [U-13C] glucose and K15NO3. Spin-echo difference spectroscopy showed that 13C was incorporated to a level of about 50% and 15N to about 98%. Incorporation of 13C into the peptide provided residue-specific probes of the interactions with solvent and heat stability of this ion-channel-forming peptide. All of the carbonyl carbons and the alpha-carbons of the alpha-aminoisobutyric acid [Ala(Me)] residues of alamethicin in methanol were assigned using two-dimensional and three-dimensional heteronuclear correlation experiments. Measurements of 1JC'N revealed hydrogen bonding with solvent at residues 1 and 19 at the ends of the peptide and at Gly11 in the middle. The data also support the thesis [see Juranic, N., Ilich, P. K. & Macara, S. (1995) J. Am. Chem. Soc. 117, 405-410 that intramolecular hydrogen bonds in proteins and peptides are weaker than hydrogen bonds to solvent. The sensitivity of alamethicin carbonyl and proton chemical shifts to perturbation by dimethyl sulfoxide correlates well with the calculated solvent accessibilities of the carbonyls in the crystal structures and reveals residues in the middle of the peptide and at the C-terminus which interact with solvent. Taken together with the 1JC'N measurements, the data support a model in which hydrogen bonding to solvent at the Gly11/Leu12 amide could provide a site of hydration in the interior of the alamethicin channel structure. The temperature dependencies of the carbonyl chemical shifts support the suggestion that the peptide is flexible in the regions where solvent interacts with the backbone of the peptide. The linear temperature dependence of the carbonyl chemical shifts and molar ellipticity indicate that, due to steric constraints at the Ala(Me) residues, the peptide folding/unfolding transition is non-cooperative and that the peptide is remarkably heat stable.