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Biocatalysis in high-concentration organic solvents (OSs) offers many advantages, but realizing this process remains a huge challenge. An R-selective ω-amine transaminase variant (AcATA M2 ) exhibited high activity toward 50 g/L pro-sitagliptin ketone 1-[1-piperidinyl]-4-[2,4,5-trifluorophenyl]-1,3-butanedione (PTfpB). However, AcATA M2 displayed unsatisfactory organic-cosolvent resistance against high-concentration dimethyl sulfoxide (DMSO), which is required to enhance the solubility of the hydrophobic substrate PTfpB. Located in the substrate-binding tunnel, enzyme gates are structural elements that undergo reversible conformational transitions, thus affecting the accessibility of the binding pocket to solvent molecules. Depending on the conformation of the enzyme gates, one can define an open or closed conformation on which the enzyme activity in OSs may depend. To enhance the DMSO resistance of AcATA M2 , we identified the beneficial residues at the "enzyme gate" region via computational analysis, alanine scanning, and site-saturation mutagenesis. Two beneficial variants, namely, AcATA M2 F56D and AcATA M2 F56V , not only displayed improved enzyme activity but also exhibited enhanced DMSO resistance (the half-life value increased from 25.71 to 42.49 h under 60% DMSO). Molecular dynamic simulations revealed that the increase in DMSO resistance was mainly caused by the decrease in the number of DMSO molecules in the substrate-binding pocket. Moreover, in the kilogram-scale experiment, the conversion of 80 g/L substrate was increased from 50% (AcATA M2 ) to 85% (M2 F56D in 40% DMSO) with a high e.e. of >99% within 24 h., (© 2021 Wiley Periodicals LLC.)

Radiolabelling with short half-lives radionuclides (e.g., fluorine-18 and carbon-11) must be as efficient and as fast as possible. Nucleophilic radiofluorinations and radiomethylations are conducted in polar aprotic solvents, such as dimethylsulfoxyde (DMSO), N,N-dimethylformamide (DMF) and N,N-dimethylacetamide (DMA), at high temperature. Those solvents are classified as toxic according to the ICH guidelines and must be evaluated in drug such as radiopharmaceuticals. Headspace gas chromatography is the standard method for the quantification of residual solvents but is not optimized for a rapid quantification of low vapor pressure solvents such as DMSO, DMF and DMA in radiopharmaceuticals. Direct injection gas chromatography is an interesting option without incubation step but the analysis run-time remains beyond 10 min long. In consequence, we developed a very simple ultra-high performance liquid chromatography method coupled with UV detection. Following the EMA requirements, we successfully validated a 3-min run-time analysis for quantification of three solvents in short half-lives radiopharmaceuticals. We currently use this method for the quality control of radiopharmaceuticals produced in our PET center., (© 2021 John Wiley & Sons, Ltd.)

Fungal unspecific peroxygenases (UPOs) are efficient biocatalysts that insert oxygen atoms into nonactivated C-H bonds with high selectivity. Many oxyfunctionalization reactions catalyzed by UPOs are favored in organic solvents, a milieu in which their enzymatic activity is drastically reduced. Using as departure point the UPO secretion mutant from Agrocybe aegerita (PaDa-I variant), in the current study we have improved its activity in organic solvents by directed evolution. Mutant libraries constructed by random mutagenesis and in vivo DNA shuffling were screened in the presence of increasing concentrations of organic solvents that differed both in regard to their chemical nature and polarity. In addition, a palette of neutral mutations generated by genetic drift that improved activity in organic solvents was evaluated by site directed recombination in vivo. The final UPO variant of this evolutionary campaign carried nine mutations that enhanced its activity in the presence of 30% acetonitrile (vol/vol) up to 23-fold over PaDa-I parental type, and it was also active and stable in aqueous acetone, methanol and dimethyl sulfoxide mixtures. These mutations, which are located at the surface of the protein and in the heme channel, seemingly helped to protect UPO from harmful effects of cosolvents by modifying interactions with surrounding residues and influencing critical loops., (© 2021 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals LLC.)

The sensing mechanism of a fluoride-anion probe BODIPY-amidothiourea (1c) has been elucidated through the density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. The theoretical study indicates that in the DMSO/water mixtures the fluorescent sensing has been regulated by the fluoride complex that formed between the probe 1c/two water molecules and the fluoride anion, and the excited-state intermolecular hydrogen bond (H-B) plays an important role in the fluoride sensing mechanism. In the first excited state, the H-Bs of the fluoride complex 1cFH 2 are overall strengthened, which induces the weak fluorescence emission. In addition, molecular orbital analysis demonstrates that 1cFH 2 has more obvious intramolecular charge transfer (ICT) character in the S 1 state than 1cH 2 formed between the probe 1c and two water molecules, which also gives reason to the weaker fluorescence intensity of 1cFH 2 . Further, our calculated UV-vis absorbance and fluorescence spectra are in accordance with the experimental measurements. © 2018 Wiley Periodicals, Inc., (© 2018 Wiley Periodicals, Inc.)

Large-scale detection of ubiquitination sites in whole cell proteomes using nano-liquid chromatography coupled to tandem mass spectrometry is a well-established technique that has deepened the understanding of protein degradation processes in eukaryotic cells. Ubiquitination sites are usually identified by detection of Lys-ɛ-Gly-Gly (K-ɛ-GG)-remnant peptides, which are generated by tryptic digestion of proteomes. We show in this application note that dimethyl sulfoxide addition to the liquid chromatography mobile phase enhances identification rates of K-ɛ-GG peptides by more than 100% due to an increase of peptide signal intensities. The gain in the number of ubiquitination site identifications exceeds by far the gain that has been published for other posttranslational modifications, namely, phosphorylation and acetylation., (Copyright © 2017 John Wiley & Sons, Ltd.)

Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. These FG-domain repeats exhibit differing cohesiveness character and differ from least (FG) to most (GLFG) cohesive. The designed FG-Nup is a 25 AA model peptide containing a noncohesive FG-motif flanked by two cohesive GLFG-motifs (WT peptide). Complete NMR-based ensemble characterization of this peptide along with a control peptide with an F>A substitution (MU peptide) are discussed. Ensemble characterization of the NMR-determined models suggests that both the peptides do not have consistent secondary structures and continue to be disordered. Nonetheless, the role of cohesive elements mediated by the GLFG motifs is evident in the WT ensemble of structures that are more compact than the MU peptide. The approach presented here allows an alternate way to investigate the specific roles of distinct amino acid motifs that translate into the long-range organization of the ensemble of structures and in general on the nature of IDPs., (© 2017 Wiley Periodicals, Inc.)

Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity., (© 2016 Wiley Periodicals, Inc.)

Catalysis of the aldol reaction between cyclohexanone and 4-nitrobenzaldehyde by mixtures of L-Arg and of L-Glu in wet dimethyl sulfoxide (DMSO) takes place with higher enantioselectivity (up to a 7-fold enhancement in the anti-aldol for the 1:1 mixture) than that observed when either L-Glu or L-Arg alone are used as the catalysts. These results can be explained by the formation of a catalytically active hydrogen-bonded complex between both amino acids, and demonstrate the possibility of positive cooperative effects in catalysis by two different α-amino acids. Chirality 28:599-605, 2016. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

[(18) F]Fluoroacetaldehyde is a biocompatible prosthetic group that has been implemented pre-clinically using a semi-automated remotely controlled system. Automation of radiosyntheses permits use of higher levels of [(18) F]fluoride whilst minimising radiochemist exposure and enhancing reproducibility. In order to achieve full-automation of [(18) F]fluoroacetaldehyde peptide radiolabelling, a customised GE Tracerlab FX-FN with fully programmed automated synthesis was developed. The automated synthesis of [(18) F]fluoroacetaldehyde is carried out using a commercially available precursor, with reproducible yields of 26% ± 3 (decay-corrected, n = 10) within 45 min. Fully automated radiolabelling of a protein, recombinant human interleukin-1 receptor antagonist (rhIL-1RA), with [(18) F]fluoroacetaldehyde was achieved within 2 h. Radiolabelling efficiency of rhIL-1RA with [(18) F]fluoroacetaldehyde was confirmed using HPLC and reached 20% ± 10 (n = 5). Overall RCY of [(18) F]rhIL-1RA was 5% ± 2 (decay-corrected, n = 5) within 2 h starting from 35 to 40 GBq of [(18) F]fluoride. Specific activity measurements of 8.11-13.5 GBq/µmol were attained (n = 5), a near three-fold improvement of those achieved using the semi-automated approach. The strategy can be applied to radiolabelling a range of peptides and proteins with [(18) F]fluoroacetaldehyde analogous to other aldehyde-bearing prosthetic groups, yet automation of the method provides reproducibility thereby aiding translation to Good Manufacturing Practice manufacture and the transformation from pre-clinical to clinical production., (Copyright © 2016 The Authors. Journal of Labelled Compounds and Radiopharmaceuticals published by John Wiley & Sons, Ltd.)

Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation β2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation β, but the conformation β2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016., (© 2016 Wiley Periodicals, Inc.)

This article describes recent developments in C3 -symmetric tris-urea low-molecular-weight gelators and their applications. The C3 -symmetric tris-ureas are excellent frameworks to form supramolecular polymers through noncovalent interactions. In organic solvents, hydrophobic tris-ureas form supramolecular gels. Amphiphilic tris-ureas form supramolecular gels in aqueous media. Functional supramolecular gels were prepared by introducing appropriate functional groups into the outer sphere of tris-ureas. Supramolecular hydrogels obtained from amphiphilic tris-ureas were used in the electrophoresis of proteins. These electrophoreses results showed several unique characteristics compared to typical electrophoreses results obtained using polyacrylamide matrices., (© 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (DMSO) induces the selective conversion of α-helix motifs into the poly(L-proline) II (PPII) helix conformation in an array of proteins, while β-sheets remain mostly unaffected. Human serum albumin (HSA), a highly α-helical protein, underwent the most dramatic changes and, therefore, was selected as a model for further investigations into the mechanism of this conformational change. Herein we report the use of two-dimensional ROA correlation analysis applying synchronous, autocorrelation, and moving windows approaches in order to understand the conformational transitions in HSA as a function of DMSO concentration. Our results indicate that the destabilization of native α-helix starts at DMSO concentrations as little as 20% in water (v/v), with the transition to PPII helix being complete at ~80% DMSO. These results clearly indicate that any protein preparation containing relatively low concentrations of DMSO should consider possible disruptions in α-helical domains., (© 2014 Wiley Periodicals, Inc.)

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent, are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on (13)Cα, (1)Hα, and (1)HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water)., (Copyright © 2013 Wiley Periodicals, Inc.)

The N- or O-methylation reactions of compounds bearing amide, aniline, or phenol moieties using iodo[(11) C]methane (1) with the aid of a base are frequently applied to the preparation of (11) C-labeled radiopharmaceuticals. Although sodium hydride and alkaline metal hydroxides are commonly employed as bases in these reactions, their poor solubility properties in organic solvents and hydrolytic activities have sometimes limited their application and made the associated (11) C-methylation reactions difficult. In contrast to these bases, tetrabutylammonium fluoride (TBAF) is moderately basic, highly soluble in organic solvents, and weakly nucleophilic. Although it was envisaged that TBAF could be used as the preferred base for (11) C-methylation reactions using 1, studies concerning the use of TBAF to promote (11) C-methylation reactions are scarce. Herein, we have evaluated the efficiency of the (11) C-methylation reactions of 13 model compounds using TBAF and 1. In most cases, the N-(11) C-methylations were efficiently promoted by TBAF in dimethyl sulfoxide at ambient temperature, whereas the O-(11) C-methylations required heating in some cases. Comparison studies revealed that the efficiencies of the (11) C-methylation reactions with TBAF were comparable or sometimes greater than those conducted with sodium hydride. Based on these results, TBAF should be considered as the preferred base for (11) C-methylation reactions using 1., (Copyright © 2013 John Wiley & Sons, Ltd.)

Previous work on elastin-like polypeptides (ELPs) made of hydrophobic amino acids of the type XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) has consistently shown that differing dominant supramolecular structures were formed when the suspending media were varied: helical, amyloid-like fibers when suspended in water and globules evolving into "string of bead" structures, poly(ValGlyGlyValGly), or cigar-like bundles, poly(ValGlyGlyLeuGly), when suspended in methyl alcohol. Comparative experiments with poly(LeuGlyGlyValGly) have further indicated that the interface energy plays a significant role and that solvation effects act in concomitance with the intrinsic aggregation propensity of the repeat sequence. Continuing our investigation on ELPs using surface (X-ray photoelectron spectroscopy, atomic force microscopy) and bulk (circular dichroism, Fourier transform infrared spectroscopy) techniques for their characterization, here we have compared the effect of suspending solvents (H(2)O, dimethylsulfoxide, ethylene glycol, and MeOH) on poly(ValGlyGlyValGly), the polypeptide most inclined to form long and well-refined helical fibers in water, searching for the signature of intermolecular interactions occurring between the polypeptide chains in the given suspension. The influence of sequence specificities has been studied by comparing poly(ValGlyGlyValGly) and poly(LeuGlyGlyValGly) with a similar degree of polymerization. Deposits on substrates of the polypeptides were characterized taking into account the differing evaporation rate of solvents, and tests on their stability in ultra high vacuum were performed. Finally, combining experimental and computational studies, we have revaluated the three-dimensional modeling previously proposed for the supramolecular assembly in water of poly(ValGlyGlyValGly). The results were discussed and rationalized also in the light of published data., (Copyright © 2012 Wiley Periodicals, Inc.)

The continually growing list of critical glycosylation-related processes has made analytical methodology for detailed glycan characterization an area of increasing interest. Glycosylation is a post translational modification of unsurpassed complexity due to the variety of compositions and linkages formed by these biopolymers. Structural characterization of glycan isomers has been achieved using ion trap mass spectrometry and MS(n) of released, permethylated glycans. However, N- and O-glycans require different sample preparation strategies; and release of the glycans may be hindered, result in degradation of the glycan, and/or produce limited yields of permethylated product. In the current report, we demonstrate universal proteolysis of both N- and O-linked glycoproteins to individual glycoamino acids. These samples were shown to be directly amenable to permethylation and MS(n) analysis for isomeric structural determination. Universal proteolysis and permethylation provides an identical sample preparation strategy for both classes of glycans that avoids potential pitfalls of commonly used release methods. This methodology should be applicable to all glycoproteins and serve as an alternative to glycan release for MS(n) branching analysis. Published 2013. This article is a U.S. Government work and is in the public domain in the USA., (Published 2013. This article is a U.S. Government work and is in the public domain in the USA.)

Dimethyl sulfoxide (DMSO) is commonly used in preclinical studies of animal models of high-grade glioma as a solvent for chemotherapeutic agents. A strong DMSO signal was detected by single-voxel MRS in the brain of three C57BL/6 control mice during a pilot study of DMSO tolerance after intragastric administration. This led us to investigate the accumulation and wash-out kinetics of DMSO in both normal brain parenchyma (n=3 control mice) by single-voxel MRS, and in 12 GL261 glioblastomas (GBMs) by single-voxel MRS (n=3) and MRSI (n=9). DMSO accumulated differently in each tissue type, reaching its highest concentration in tumors: 6.18 ± 0.85 µmol/g water, 1.5-fold higher than in control mouse brain (p<0.05). A faster wash-out was detected in normal brain parenchyma with respect to GBM tissue: half-lives of 2.06 ± 0.58 and 4.57 ± 1.15 h, respectively. MRSI maps of time-course DMSO changes revealed clear hotspots of differential spatial accumulation in GL261 tumors. Additional MRSI studies with four mice bearing oligodendrogliomas (ODs) revealed similar results as in GBM tumors. The lack of T(1) contrast enhancement post-gadolinium (gadopentetate dimeglumine, Gd-DTPA) in control mouse brain and mice with ODs suggested that DMSO was fully able to cross the intact blood-brain barrier in both normal brain parenchyma and in low-grade tumors. Our results indicate a potential role for DMSO as a contrast agent for brain tumor detection, even in those tumors 'invisible' to standard gadolinium-enhanced MRI, and possibly for monitoring heterogeneities associated with progression or with therapeutic response., (Copyright © 2012 John Wiley & Sons, Ltd.)

We have firstly demonstrated the renaturation process of dissociated single chains of lentinan (s-LNT) and the variable conformations of the renatured LNT (r-LNT). The results from ultrasensitive differential scanning calorimetry and circular dichroism revealed that the variable structures including perfect triple helix, defective triple helix containing duplex segment, and single chains occurred in the renaturation of s-LNT, depending on the renaturation time, solvent composition, molecular weight, and the mode of renaturation. When water was added into s-LNT/dimethylsulfoxide (DMSO) to reach 95% (v/v), the classic low-temperature intra-triple-helical conformational transition at ∼10(°) C (T(1)) appeared within 4 h, indicative of a rapid reconstruction of triple helical structure. Besides, one newly endothermic peak at ∼43(°) C (T(2)) simultaneously occurred, which was first ascribed to the melting of duplex segment in the imperfect triplex. The duplex stretches disappeared when DMSO reached 50%, in which single chains coexisted with triplex. Moreover, the duplex segment disappeared by slowly dropping water into s-LNT/DMSO. This work suggested that the structure of r-LNT could be controllable, and provided important information for their successful development and application in polymer and life science., (Copyright © 2012 Wiley Periodicals, Inc.)

Lentinan (β-(1→3)-D-glucan) was found to be successfully fractionated by the mixture of dimethyl sulfoxide (DMSO) and lithium chloride (LiCl) as a solvent and acetone as a precipitant. Light scattering and viscosity measurements were made on solutions of fractionated samples in pure DMSO and 0.2M LiCl/DMSO in the range of the molecular weight M(w) from 21.7 × 10(4) to 84.7 × 10(4) . The values of M(w) in both solvents were almost the same, but the remarkable difference between the values of intrinsic viscosity [η] demonstrated that the LiCl/DMSO solvent greatly enhances the stiffness of the lentinan backbone. The observed intrinsic viscosity [η] was analyzed by the Yoshizaki-Nitta-Yamakawa theory of a worm-like chain, and the persistence length q and molecular weight per unit contour length M(L) were determined roughly as 6.0 nm and 890 g nm(-1) in 0.2M LiCl/DMSO, and 5.1 nm and 890 g nm(-1) in pure DMSO, respectively. This slightly larger persistent length in 0.2M LiCl/DMSO also confirmed the higher stiffness of lentinan enhanced by the LiCl/DMSO solvent. The enhancement of the chain stiffness was ascribed to the electrostatic repulsion because of the hydrogen bonding of the hydroxyl protons of lentinan with the chloride ion, which is in turn associated with the Li(+) (DMSO)(n) macrocation complex. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 840-845, 2012., (Copyright © 2012 Wiley Periodicals, Inc.)

Cells are routinely cryopreserved for investigative and therapeutic applications. The most common cryoprotective agent (CPA), dimethyl sulfoxide (DMSO), is toxic, and must be removed before cells can be used. This study uses a microfluidic device in which three streams flow vertically in parallel through a rectangular channel 500 µm in depth. Two wash streams flow on either side of a DMSO-laden cell stream, allowing DMSO to diffuse into the wash and be removed, and the washed sample to be collected. The ability of the device to extract DMSO from a cell stream was investigated for sample flow rates from 0.5 to 4.0 mL/min (Pe = 1,263-10,100). Recovery of cells from the device was investigated using Jurkat cells (lymphoblasts) in suspensions ranging from 0.5% to 15% cells by volume. Cell recovery was >95% for all conditions investigated, while DMSO removal comparable to a previously developed two-stream device was achieved in either one-quarter the device length, or at four times the flow rate. The high cell recovery is a ~25% improvement over standard cell washing techniques, and high flow rates achieved are uncommon among microfluidic devices, allowing for processing of clinically relevant cell populations., (Copyright © 2012 Wiley Periodicals, Inc.)

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ϕ-ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures., (© 2011 Wiley Periodicals, Inc.)

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally., (Copyright © 2011 Wiley Periodicals, Inc.)

Molecular dynamics simulations of charged and neutral solutes in dimethyl sulfoxide (DMSO)-chloroform mixtures reveal pronounced nonideality in the solute diffusion with changes of composition of the mixtures. The diffusion coefficient of the anionic solute first decreases, passes through a minimum at DMSO mole fraction of about 0.50, and then increases to reach its value for pure DMSO. The diffusion coefficients of the cationic and neutral solutes are found to decrease with increase in DMSO content of the solvent mixture. The extent of nonideality in the diffusion and orientational relaxation of solvent molecules is found to be somewhat stronger than that in diffusion of the anionic solute in these mixtures. We have also calculated the relaxation of hydrogen bonds formed between DMSO and chloroform molecules. The lifetimes of DMSO-chloroform hydrogen bonds are found to increase monotonically with increase in DMSO concentration. The average number of hydrogen bonds and their average energies are also computed. It is found that an increase in DMSO concentration causes a decrease in the number of DMSO-chloroform hydrogen bonds per DMSO or chloroform molecules but increases the strength of these hydrogen bonds., (Copyright © 2011 Wiley Periodicals, Inc.)

The chemical tropospheric dimethyl sulfide (DMS, CH3SCH3) degradation involves several steps highly dependent on the environmental conditions. So, intensive efforts have been devoted during the last years to enhance the understanding of the DMS oxidation mechanism under different conditions. The reaction of DMS with OH is considered to be the most relevant process that initiates the whole oxidation process. The experimental observations have been explained by a two-channel mechanism consisting of a H-abstraction process leading to CH3S(O)CH3 and HO2 and an addition reaction leading to the DMS·OH adduct. In the presence of O2, the DMS·OH adduct is competitively scavenged increasing the contribution of the addition channel to the overall DMS oxidation. Recent experimental measurements have determined from a global fit that the rate constant of this scavenging process is independent of pressure and temperature but this rate constant cannot be directly measured. In this article, a variational transition-state theory calculation of the low- and high-pressure rate constants for the reaction between DMS·OH and O2 has been carried out as a function of temperature. Our proposal is that the slight temperature dependence of the scavenging rate constant can only be explained if the H-abstraction bottleneck is preceded by a dynamical bottleneck corresponding to the association process between the DMS·OH adduct and the O2 molecule. The agreement between the low-pressure and high-pressure rate constants confirms the experimental observations., (Copyright © 2011 Wiley Periodicals, Inc.)

Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.

The mononuclear complex Pd(1-TosC-N3)(2)Cl(2) (2) containing 1-(p-toluenesulfonyl)cytosine (1) as a ligand, as well as dinuclear complexes Pd(2)(1-TosC(-)-N3,N4)(4) (3) and Pd(2)(1-TosC(-)-N3,N4)(2)DMSO(2)Cl(2) (4) containing the ligand anion (1-TosC(-)), was mass analyzed by electrospray ionization ion trap MS/MS and high resolution MS. Complexes 3 and 4 were obtained by recrystallization of 2 from DMF and DMSO, respectively. The behavior of complex 2 in different solutions was monitored by electrospray ionization mass spectrometry (ESI-MS). Under the applied ESI-MS conditions, complex 2 in methanol reorganized itself dominantly as new complex 3 and the solvent did not coordinate the formed species. In H(2)O/DMSO, CH(3)CN/DMSO and CH(3)OH/DMSO solutions, complex 2 formed several new species with solvent molecules involved in their structure, e.g. complex 4 was formed as the major product. The newly formed species were also examined by LC-MS-DAD, confirming the solvent induced reorganization and the solution instability of complex 2., (Copyright 2009 John Wiley & Sons, Ltd.)

Hepcidin is a four disulfide 25-residue peptide hormone which has a central role in the regulation of iron homeostasis. To support studies on hepcidin we have sought to establish reliable and robust synthetic methods for the preparation of correctly folded materials. While correctly-folded hepcidin has good aqueous solubility, we have found that its direct synthetic precursor, linear (reduced) hepcidin peptide, is resistant to solubilization, prone to precipitation at pH > or = 6, and thus difficult to fold efficiently. Attempts to directly fold either the crude or purified linear hepcidin peptide by air or DMSO oxidation methods under basic conditions were ineffective. However, addition of a glutathione redox pair system improved folding of purified linear hepcidin at mild basic pH (pH 7.5). Under acidic conditions, it was possible to oxidatively fold both crude and purified hepcidin using a polymer-supported oxidizing strategy. Peptide precipitation was also avoided under acidic conditions. Isolated folding yields of human hepcidin under acidic polymer-assisted conditions were superior to yields under basic folding conditions. These studies enabled identification of a reliable synthetic route for correctly-folded hepcidin.

Four linear thiourea anion receptors (1-3) derived from simple amino acid have been synthesized and their bonding properties with various chiral N-protected amino acid anions were examined by using UV-vis and fluorescence titration experiments. Receptors 1a, 2, and 3 exhibit excellent enantioselective recognition abilities towards N-Boc-protected alanine anion in the UV-vis spectra, obvious difference in the color of solution indicate that the enantiomers of N-Boc-alanine anion could be distinguished by naked eye directly. Receptor 1a is also found to carry out enantioselective fluorescent recognition of the N-acetyl-glutamate. (1)H NMR experiments suggest that hydrogen-bonding interaction between the host and guest is the main factor in the recognition process., ((c) 2008 Wiley-Liss, Inc.)

The relative importance of the reaction pathways and thus the product yields in the dimethyl sulfide (DMS) degradation scheme initiated by the hydroxyl (OH) radical has been said to be influenced by the content of nitrogen oxides (NO(x)) in chamber experiments. In this study, ab initio and density functional electronic structure calculations of all the possible reaction pathways corresponding to the reaction process initiated by DMS-OH + oxygen (O(2)), leading to the formation of the dimethyl sulfoxide (DMSO) product in the presence of NO(x) (NO and NO(2)), are carried out for the first time. The results for the different pathways are compared with the objective of inferring their kinetic relevance in the laboratory experiments that measure DMSO formation yields. Our theoretical results clearly show the existence of NO(x)-dependent pathways leading to the formation of DMSO in addition to O(2)-dependent channels. So then, NO(x)-containing conditions would have to modify the relative importance of the addition channel in the DMS oxidation process., ((c) 2008 Wiley Periodicals, Inc.)

A rapid capillary electrophoresis procedure was developed for determining the anti-cancer components, camptothecins, in Nothapodytes foetida. The hydrophobic compound was extracted from plant tissue (ca. 1 mL of DMSO for 100 mg of dried plant tissue) with a water-miscible organic solvent, DMSO, at elevated temperature (60 degrees C). The extract was directly injected into the separation capillary (untreated fused silica, 34 cm in length, 75 microm i.d.) and analysed in MEKC mode (369 nm). Within 5 min of migration, camptothecins were successfully separated and quantified by adding organic modifiers to the running buffer (20% DMSO, 90 mm SDS in 10 mm borate buffer, pH 8.60). The linear dynamic range for camptothecin was from 5 to 400 microg/mL. This method was proven to be very suitable for monitoring the amount of camptothecins during the cultivation of the medicinal plant., (Copyright 2007 John Wiley & Sons, Ltd.)

The C-terminally amidated CRF antagonist astressin binds to CRF-R1 or CRF-R2 receptors with low nanomolar affinity while the corresponding astressin-acid has >100 times less affinity. To understand the role of the amide group in binding, the conformations of astressin-amide and astressin-acid were studied in DMSO using NMR techniques. The 3D NMR structures show that the backbones of both analogs prefer an alpha-helical conformation, with a small kink around Gln(26). However, astressin-amide has a well-defined helical structure from Leu(27) to Ile(41) and a conformation very similar to the bioactive conformation reported by our group (Grace et al., Proc Natl Acad Sci USA 2007, 104, 4858-4863). In contrast, astressin-acid has an irregular helical conformation from Arg(35) onward, including a rearrangement of the side chains in that region. This structural difference highlights the crucial role of the C-terminal amidation for stabilization of astressin's bioactive conformation.

A simple and sensitive RP-HPLC-UV method was developed and validated for simultaneous determination of atenolol and propranolol and subsequently applied to investigate the effect of dimethyl sulfoxide in rat in situ intestinal permeability studies. Atenolol (400 microm) and propranolol (100 microm) were perfused in the small intestine of anaesthetized (pentobarbitone sodium 60 mg/kg, i.p.) male Sprague-Dawley rats either in the presence (1, 3 and 5%) or in the absence of dimethyl sulfoxide. There was no significant alteration (p > 0.05) in the permeability of atenolol and propranolol, which indicated there was no effect of various concentrations of dimethyl sulfoxide (1-5%) on the membrane integrity of the rat intestinal tissues. The analytical method was validated on a C(4) column with a mobile phase comprising ammonium acetate buffer (pH 3.5, 0.02 m) and acetonitrile in the ratio of 30:70 (v/v) at a flow rate of 1.0 mL/min. The validated method was found to be accurate and precise and stability studies were carried out at different storage conditions and both analytes were found to be stable. These findings are applicable for determining the absorbability of water-insoluble drugs and new chemical entities for the purpose of classifying them in the biopharmaceutical classification system., ((c) 2006 John Wiley & Sons, Ltd.)

Cytochrome P450 BM-3 from Bacillus megaterium is an extensively studied enzyme for industrial applications. A major focus of current protein engineering research is directed to improving the catalytic performance of P450 BM-3 toward nonnatural substrates of industrial importance in the presence of organic solvents or cosolvents. For the latter reason, it is important to study the effect of organic cosolvent molecules on the structure and dynamics of the enzyme, in particular, the effect of cosolvent molecules on the active site's structure and dynamics. In this paper, we have studied, using molecular dynamics (MD) simulations, the F87A mutant of P450 BM-3 in the presence of DMSO as cosolvent, to understand the role of the F87A substitution for its catalytic activity. This mutant exhibits an altered regioselectivity and substrate specificity compared with wild-type; however, it has lower tolerance toward DMSO. The simulation results offer an explanation for the DMSO sensitivity of the F87A mutant. Our simulation results show that the F87 side chain prevents the disturbance of the water molecule bound to the heme iron by DMSO molecules. The absence of the phenyl ring in F87A mutant promotes interactions of the DMSO molecule with the heme iron resulting in water displacement by DMSO at the catalytic heme center., ((c) 2006 Wiley Periodicals, Inc.)

Pro-Hyp-Gly is a characteristic amino acid sequence found in fibrous collagens, and (Pro-Hyp-Gly)(10), which has been widely used as a collagen-model peptide, forms a stable triple-helical structure. Here, we synthesized polypeptides consisting of the Pro-Hyp-Gly sequence by direct poly-condensation of (Pro-Hyp-Gly)(n), where n=1, 5, and 10, using 1-hydroxybenzotriazole and 1-ethyl-3-(3-dimethyl-aminopropyl)-carbodiimide hydrochloride in both phosphate buffer (pH=7.4) and dimethylsulfoxide (DMSO) solutions for 48 h at 20 degrees C. The reaction of (Pro-Hyp-Gly)(5) and (Pro-Hyp-Gly)(10) in DMSO successfully gave polypeptides with molecular weights over 10,000, whereas low molecular weight products were obtained by reaction in phosphate buffer (pH=7.4). In contrast, Pro-Hyp-Gly at a concentration of 50 mg/mL in phosphate buffer (pH=7.4) gave polypeptides with molecular weights over 10,000. The Fourier transform infrared (FTIR) and (1)H nuclear magnetic resonance (NMR) spectra of poly(Pro-Hyp-Gly)(10) revealed that the polymerization of (Pro-Hyp-Gly)(10) described in this report had no side reactions. Each polypeptide obtained shows a collagen-like triple-helical structure, and the triple-helical structures of poly(Pro-Hyp-Gly) and poly(Pro-Hyp-Gly)(10) were stable up to T=80 degrees C, which suggests that the high molecular weight promotes stability of the triple-helical structure, in addition to the high Hyp content. Furthermore, transmission electron microscopy (TEM) observations show that poly(Pro-Hyp-Gly)(10) aggregates to form nanofiber-like structures about 10 nm in width, which suggests that a Pro-Hyp-Gly repeating sequence contains enough information for triple-helix formation, and for subsequent nanofiber-like structure formation., ((c) 2005 Wiley Periodicals, Inc. Biopolymers 79: 163-172, 2005.)

Long-term storage of platelets is infeasible due to platelet activation at low temperatures. In an effort to address this problem, we evaluated the effectiveness of a formulation combining trehalose and phosphate in protecting platelet structure and function following cryopreservation. An annexin V binding assay was used to quantify the efficacy of the trehalose and phosphate formulation in suppressing platelet activation during cryopreservation. Of the platelets cryopreserved with the trehalose plus phosphate formulation, 23% +/- 1.2% were nonactivated, compared with 9.8% +/- 0.26% nonactivated following cryopreservation with only trehalose. The presence of both trehalose and phosphate in the cryopreservation medium is critical for cell survival and preincubation in trehalose plus phosphate solutions further enhances viability. The effectiveness of trehalose plus phosphate in preserving platelets in a nonactivated state is comparable to 6% dimethyl sulfoxide (Me(2)SO). Measurements of platelet metabolic activity using an alamarBlue assay also established that trehalose plus phosphate is superior to trehalose alone. Finally, platelets protected by the trehalose plus phosphate formulation exhibit similar aggregation response upon thrombin addition as fresh platelets, but an increase of cytosolic calcium concentration upon thrombin addition was not observed in the cryopreserved platelets. These results suggest that trehalose and phosphate protect several aspects of platelet structure and function during cryopreservation, including an intact plasma membrane, metabolic activity, and aggregation in response to thrombin, but not intracellular calcium release in response to thrombin.

Solvent molecules play an important role for the structural and dynamical properties of proteins. A major focus of current protein engineering is the development of enzymes that are catalytically active in the presence of organic solvents. The monooxygenase P450 BM-3 is one of the best-studied enzymes and promising for industrial applications but with limited activity in the presence of organic solvents or cosolvents. To gain insights into the structural and dynamical properties of the heme domain of this enzyme in solution, molecular dynamics simulations in pure water and in a 14% DMSO/water mixture were performed. The results of the simulations show overall similar structural fluctuations in both solvent systems, with no indication of partial or global unfolding. In 14% DMSO, the regions comprising the helices E, F, and the EF loop (implicated in controlling the entry to the active site channel) undergo a large shift. Significant changes were also observed near the active site access channel at the residue R47. During the simulation, no DMSO molecule penetrated the active site. However, a significant accumulation of DMSO molecules close to the substrate-binding site and to the Flavin Mononucleotide (FMN) reductase domain interface was observed., (Copyright 2005 by Wiley Periodicals, Inc)

Cytochrome p450 BM-3 (EC 1.14.14.1) catalyzes the hydroxylation and/or epoxidation of a broad range of substrates, including alkanes, alkenes, alcohols, fatty acids, amides, polyaromatic hydrocarbons, and heterocycles. For many of these notoriously water-insoluble compounds, p450 BM-3's K(m) values are in the millimolar range. Polar organic cosolvents are therefore added to increase substrate solubility and achieve high catalytic efficiency. Using p450 BM-3 as a catalyst for these important transformations requires that we improve its ability to tolerate the cosolvents. By directed evolution, we improved the activity of p450 BM-3 in the presence of dimethylsulfoxide (DMSO) and tetrahydrofuran (THF), achieving increases in specific activity up to 10-fold in 2% (v/v) THF and 6-fold in 25% (v/v) DMSO. The engineered p450 BM-3's are also significantly more resistant to acetone, acetonitrile, dimethylformamide, and ethanol as cosolvents in the reaction., (Copyright 2004 Wiley Periodicals, Inc.)

The major challenge in developing cryopreservation protocols for microencapsulated cells is that the relatively large size (300-400 microm) and the fragile semipermeable membrane of microcapsules makes them particularly prone to cryodamage. Rapid-cooling cryopreservation protocols with high DMSO concentrations (3.5M, 25% v/v) resulted in low post-thaw cell viability (<10%), which did not improve with higher concentrations (4.5M, 32% v/v) and longer exposure to DMSO, even though the majority of microcapsules (60-80%) remained intact. Subsequent investigations of slow cooling with a range of DMSO and EG concentrations resulted in a much higher post-thaw cell viability (80-85%), with the majority of the microcapsules remaining intact ( approximately 60%) when DMSO was used at a concentration of 2.8M (20% v/v) and EG at a concentration of 2.7M (15% v/v). The presence of 0.25M sucrose significantly improved post-thaw cell viability upon slow cooling with 2.8M (20% v/v) DMSO, although it had no effect on microcapsule integrity. Multistep exposure and removal of sucrose did not significantly improve either post-thaw cell viability or microcapsule integrity, compared to a single-step protocol. Ficoll 20% (w/v) also did not significantly improve post-thaw cell viability and microcapsule integrity. Hence, the optimal condition for microcapsule cryopreservation developed in this study is slow cooling with 2.8M (20% v/v) DMSO and 0.25M sucrose., (Copyright 2003 Wiley Periodicals, Inc.)

The interactive effects of temperature and cosolvents on the kinetic and structural features of a carboxylesterase from the extremely thermoacidophilic archaeon Sulfolobus solfataricus P1 (Sso EST1) were examined. While dimethylformamide, acetonitrile, and dioxane were all found to be deleterious to enzyme function, dimethyl sulfoxide (DMSO) activated Sso EST1 to various extents. This was particularly true at 3.5% (v/v) DMSO, where k(cat) was 20-30% higher than at 1.2% DMSO, over the temperature range of 50-85 degrees C. DMSO compensated for thermal activation in some cases; for example, k(cat) at 60 degrees C in 3.5% DMSO was comparable to k(cat) at 85 degrees C in 1.2% DMSO. The relationship between DMSO activation and enzyme structural characteristics was also investigated. Nuclear magnetic resonance spectroscopy and circular dichroism showed no gross change in enzyme conformation with 3.5% DMSO between 50 and 80 degrees C. However, low levels of DMSO were shown to have a small yet significant change in enzyme conformation. This was evident through the reduction of Sso EST1's melting temperature and changes in the microenvironment of the enzyme's tyrosine and tryptophan residues at 3.5% versus 1.2% (v/v) solvent. Finally, activation parameter analysis based on kinetic data, at 1.2% and 3.5% DMSO, implied an increase in conformational flexibility with additional cosolvent. These results suggest the activating effect of DMSO was related to small changes in the enzyme's structure resulting in an increase in its conformational flexibility. Thus, in addition to their use for solubilizing hydrophobic substrates in water, cosolvents may also serve as activators in applications involving thermostable biocatalysts at sub-optimal temperatures., (Copyright 2002 Wiley Periodicals, Inc.)

New biomaterial related reference materials with known genotoxic properties were produced in order to study the sample preparation and in vitro genotoxicity testing of biomaterials. We incorporated genotoxic substances like benzo[a]pyrene into the biomaterial Tecoflex, a polyurethane frequently used for catheters and other applications. We demonstrated that the model compound benzo[a]pyrene is sufficiently extracted by organic solvents, whereas cell culture medium only extracts very limited quantities. By changing the medium several times during extraction the extracted amount was augmented. Using higher amounts of organic solvent in relation to the reference material's surface led to a higher recovery of extracted benzo[a]pyrene. For the in vitro genotoxicity testing using the Mammalian Cell Gene Mutation Test (HPRT test), Mammalian Chromosome Aberration Test, and bacterial umu- and SOS-tests, concentration of extracts is a prerequisite because of the low sensitivity of the test systems. Often cytotoxicity interferes with the evaluation of genotoxic effects. We demonstrated that some recommendations of the ISO 10993-Part 3 and 12,(1),(2) dealing with the biological evaluation of medical devices, seem to be insufficient, and new rules for the in vitro genotoxicity testing of biomaterials have to be established., (Copyright 2002 Wiley Periodicals, Inc.)

A statistical mechanics methodology for predicting the solution structures and populations of peptides developed recently is based on a novel method for optimizing implicit solvation models, which was applied initially to a cyclic hexapeptide in DMSO (C. Baysal and H. Meirovitch, Journal of American Chemical Society, 1998, vol. 120, pp. 800-812). Thus, the molecule has been described by the simplified energy function E(tot) = E(GRO) + summation operator(k) sigma(k)A(k), where E(GRO) is the GROMOS force-field energy, sigma(k) and A(k) are the atomic solvation parameter (ASP) and the solvent accessible surface area of atom k, respectively. In a more recent study, these ASPs have been found to be transferable to the cyclic pentapeptide cyclo(D-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO (C. Baysal and H. Meirovitch, Biopolymers, 2000, vol. 53, pp. 423-433). In the present paper, our methodology is applied to the cyclic heptapeptides axinastatin 2 [cyclo(Asn(1)-Pro(2)-Phe(3)-Val(4)-Leu(5)-Pro(6)-Val(7))] and axinastatin 3 [cyclo(Asn(1)-Pro(2)-Phe(3)-Ile(4)-Leu(5)-Pro(6)-Val(7))], in DMSO, which were studied by nmr by Mechnich et al. (Helvetica Chimica Acta, 1997, vol. 80, pp. 1338-1354). The calculations for axinastatin 2 show that special ASPs should be optimized for the partially charged side-chain atoms of Asn while the rest of the atoms take their values derived in our previous work; this suggests that similar optimization might be needed for other side chains as well. The solution structures of these peptides are obtained ab initio (i.e., without using experimental restraints) by an extensive conformational search based on E(GRO) alone and E(*)(tot), which consists of the new set of ASPs. For E(*)(tot), the theoretical values of proton-proton distances, (3)J coupling constants, and other properties are found to agree very well with the nmr results, and they are always better than those based on E(GRO)., (Copyright 2000 John Wiley & Sons, Inc.)

A formal development of the Counterion Condensation theory (CC) of linear polyelectrolytes has been performed to include specific (chemical) affinity of condensed counterions, for polyelectrolyte charge density values larger than the critical value of condensation. It has been conventionally assumed that each condensed counterion exhibits an affinity free-energy difference for the polymer, (DeltaG(aff)). Moreover, the model assumes that the enthalpic and entropic contributions to DeltaG(aff), i.e., DeltaH(aff) and DeltaS(aff), are both independent of temperature, ionic strength and polymer concentration. Equations have been derived relative to the case of the thermally induced, ionic strength dependent, conformational transition of a biopolyelectrolyte between two conformations for which chemical affinity is supposed to take place. The experimental data of the intramolecular conformational transition of the ionic polysaccharide kappa-carrageenan in dimethylsulfoxide (DMSO) have been successfully compared with the theoretical predictions. This novel approach provides the enthalpic and entropic affinity values for both conformations, together with the corresponding thermodynamic functions of nonpolyelectrolytic origin pertaining to the biopolymer backbone change per se, i.e., DeltaH(n.pol) and DeltaS(n.pol), according to a treatment previously shown to be successful for lower values of the biopolyelectrolyte linear charge density. The ratio of DeltaH(n.pol) to DeltaS(n.pol) was found to be remarkably constant independent of the value of the dielectric constant of the solvent, from formamide to water to DMSO, pointing to the identity of the underlying conformational process., (Copyright 1999 John Wiley & Sons, Inc.)

Analysis of nuclear Overhauser enhancement (NOE) intensities data of interconverting microstates of a peptide is a difficult problem in nmr. A new statistical mechanics methodology has been proposed recently, consisting of several steps: (1) potential energy wells on the energy surface of the molecule are identified (the corresponding regions are called wide microstates); (2) each wide microstate is then spanned by a Monte Carlo (MC) or molecular dynamics simulation starting from a representative structure, and the corresponding relative populations are obtained from the free energy calculated with the local states method; and (3) the overall NOEs and 3J coupling constants are obtained as averages over the corresponding contributions of the samples, weighted by the populations. Extending this methodology to cyclic peptides, we are treating here the hexapeptide cyclo(D-Pro1-Phe2-Ala3-Ser4-Phe5-Phe6) in DMSO, which was studied by Kessler et al. using nmr (Journal of the American Chemical Society, 1992, Vol. 114, pp. 4805-4818). They found that at least two structures are required to explain their NOE data, a conclusion also corroborated by our analysis (Journal of the American Chemical Society, 1998, Vol. 120, pp. 800-812) and led to a novel derivation of atomic solvation parameters (ASPs) for DMSO. Thus, the overall interactions within the peptide-solvent system are described approximately by Etot = EGRO + summation operator sigmaiAi, where EGRO is the energy of the GROMOS force field, Ai is the solvent-accessible surface area of atom i, and sigmai is the ASP. In the present paper the validity of these ASPs within the framework of the entire methodology is verified. This requires taking into account 23 microstates. A very good agreement is obtained between experimental and calculated NOEs and 3J coupling constants. The free energy based populations lead to the best results, which means that entropic effects should not be ignored. We have also studied the behavior of the internal angular fluctuations of the proton-proton vectors and discovered that they have a negligible effect on the calculated NOEs; this is due to the relatively concentrated wide microstates spanned by the MC simulations. The applicability of our ASPs to other cyclic peptides in DMSO is being studied in another work and preliminary results are discussed., (Copyright 1999 John Wiley & Sons, Inc.)

A water-soluble glucan A was isolated from the fruit body of Auricularia auricula-judae. It is composed of a backbone chain of beta-(1-->3)-linked D-glucose residues, two out of three glucose residues being substituted at C-6 positions with a single glucose unit. The weight average molecular weight Mw, number average molecular weight Mn, and intrinsic viscosity [eta] of the fractionated samples were studied at 25 degrees C in water and in dimethylsulfoxide (DMSO). The Mark-Houwink equation was established as [eta] = 6.10 x 10(-4) Mw1.14 for the glucan A having Mw ranging from 9 x 10(5) to 1.6 x 10(6) in water. The values of [eta] in water are far higher than those in DMSO, but the values of Mn measured in water are the same as those in DMSO. Analysis of Mw and [eta] in terms of the known theories for rods and wormlike chains yielded 1030 +/- 100 nm-1, 90 +/- 20 nm, 1.3 +/- 0.3 nm, and 0.26 +/- 0.03 nm for molar mass per unit contour length ML, persistence length q, diameter d, and contour length h per main-chain glucose residue, respectively. The present data suggest that glucan A dissolves in water as single-stranded helical chains and in DMSO as semiflexible chains.

The crystal structure of a dipeptide L-leucyl-L-leucine (C12H24N2O3) has been determined. The crystals are monoclinic, space group P2(1), with a = 5.434(4) A, b = 15.712(7) A, c = 11.275(2) A, beta = 100.41(1) degrees, and Z = 2. The crystals contain one molecule of dimethyl sulfoxide (DMSO) as solvent of crystallization for each dipeptide molecule. The structure has been solved by direct methods and refined to a final R index of 0.059 for 920 reflections (sin theta/lambda < or = 0.60 A-1) with I > or = 2 sigma (I). The trans peptide unit shows substantial degree of non-planarity (delta omega = 14 degrees). The peptide backbone adopts an extended conformation with torsion angles of psi 1 = 138(1) degrees, omega 1 = 166(1) degrees, phi 2 = -149.3(7) degrees, psi 21 = 164.2(7) degrees, and psi 22 = -15(1) degrees. For the first leucyl residue, the side-chain conformation is specified by the torsion angles 1 chi 1 = 176.7(7) degrees, 1 chi 21 = 62(1) degrees, 1 chi 22 = -177.4(8) degrees; the second leucyl residue adopts a sterically unfavorable conformation with 2 chi 1 = 61(1) degrees, 2 chi 21 = 97(1) degrees, and 2 chi 22 = -151(1) degrees. The packing involves head-to-tail interaction of peptide molecules and segregation of polar and nonpolar regions. The DMSO molecule is strongly hydrogen bonded to the terminal NH3+ group.

The structure of valinomycin in a range of organic solvents of varying polarity and in detergent and lipid dispersions has been studied by Fourier transform ir spectroscopy. In solvents of low polarity such as chloroform, ir spectra of valinomycin are fully consistent with the bracelet structure proposed on the basis of nmr spectroscopy, showing a single narrow amide I component attributable to the presence of beta-turns and a single band arising from nonhydrogen-bonded ester C = O groups. K+ complexation results in a downward shift in the amide I band frequency, indicating an increase in the strength of the amide hydrogen bonds, along with a shift to lower frequencies of the ester C = O absorption due to a reduction in electron density in these bonds upon complexation. Identical results were obtained with NH4+, a finding not previously reported. In solvents of both medium (CHCl3/DMSO 3:1) and high (pure DMSO) polarity, we find evidence of significant disruption of the internal hydrogen-bonding network of the peptide and the appearance of a band suggesting the presence of free amide C = O groups. In such solvents, complexation with K+ and NH4+ was not observed. The structure of valinomycin in detergent micelles resembles that in nonpolar organic solvents. However, changes were found in the amide I and ester carbonyl maxima as 2H2O penetrated the micelle which suggest significant interaction between the solvent and peptide. Complexation with K+ was reduced in cationic detergent micelles as a result of a decrease in the effective K+ concentration due to charge repulsion at the micelle surface.(ABSTRACT TRUNCATED AT 250 WORDS)