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PubMedDate not supplied

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k.

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.

Calbindins↗
PubMed2001

Biodegradation of non-desorbable naphthalene in soils.

The degradation of naphthalene was studied in soil-slurry systems, and a quantitative model was developed to evaluate the bioavailability of sorbed-phase contaminant. Four soils with different organic matter contents were used as sorbents. Two naphthalene-degrading organisms, Pseudomonas putida G7 and NCIB 9816-4, were also selected. Sorption isotherms and single and series dilution desorption studies were conducted to evaluate distribution coefficients, desorption parameters, and the amount of non-desorbable naphthalene. Biodegradation kinetics were measured in soil extract solutions and rate parameters estimated. Bioavailability assays involved establishing sorption equilibrium, inoculating the systems with organisms, and measuring naphthalene concentrations in both sorbed and dissolved phases over time. For all four soils, the sorption isotherms were linear, and desorption could be described by a model involving three types of sites: equilibrium, nonequilibrium, and non-desorption. Enhanced bioavailability, as evidenced by faster than expected degradation rates based on liquid-phase concentrations, were observed in soils with the higher sorption distribution coefficients. These observations could be described using model formulations that included solid-phase degradation. In all soils studied, degradation of non-desorbable naphthalene was observed.

Absorption↗
PubMed2004

Bioavailability of PAHs: effects of soot carbon and PAH source.

The bioavailability of 38 individual polycyclic aromatic hydrocarbon (PAH) compounds was determined through calculation of biota-sediment-accumulation factors (BSAF). BSAF values were calculated from individual PAH concentrations in freshwater mussel, marine clam, and sediment obtained from field and laboratory bioaccumulation studies. Sediment that was amended with different types of soot carbon (SC) was used in some of the bioaccumulation experiments. BSAF values for petrogenic PAH were greater than those for pyrogenic PAH (e.g., 1.57 +/- 0.53 vs 0.25 +/- 0.23, respectively), indicating that petrogenic PAH are more bioavailable than pyrogenic PAH (p < 0.05). This trend was consistent among marine and freshwater sites. Increased SC content of sediment resulted in a linear decrease in the bioavailability of pyrogenic PAHs (r2 = 0.85). The effect of increasing SC content on petrogenic PAH was negligible. SC was considered as an additional sorptive phase when calculating BSAF values, and using PAH-SC partition coefficients from the literature, we obtained unreasonably large BSAF values for all petrogenic PAH and some pyrogenic PAH. This led us to conclude that a quantitative model to assess bioavailability through a combination of organic carbon and soot carbon sorption is not applicable among field sites with a wide range of soot carbon fractions and PAH sources, at least given our current knowledge of PAH-SC partitioning. Our data offer evidence that many factors including analysis of a full suite of PAH analytes, PAH hydrophobicity, sediment organic carbon content, sediment soot carbon content, and PAH source are importantto adequately assess PAH bioavailability in the environment.

Animals↗
PubMed2003

Rejection efficiency of water quality parameters by reverse osmosis and nanofiltration membranes.

The objective of this study was to evaluate the effectiveness of reserve osmosis (RO) and nanofiltration (NF) membranes, under various solution chemistries, on water quality. The effects of organic carbon, divalent and monovalent cations, bacteria, and permeate drag on the rejection efficiencies of three different membranes were investigated through a series of laboratory bench-scale experiments. Quantitative models were successfully developed to predict the rejection of turbidity, divalent and monovalent cations, ultraviolet absorbance at 253.7 nm (UV254), and dissolved organic carbon (DOC) by membrane filtration. It was found that mechanical sieving (measured as molecular weight cutoff, MWCO) and electrostatic interactions were the most significant parameters since they were found to be important in nearly all models developed. For negatively charged membranes, under high ionic strength solution environments that repress electrostatic interaction between charged compounds and membranes, passage of compounds was mainly a function of size exclusion (i.e. MWCO). Further, of the feedwater parameters tested, bacteria concentration was observed to be the most significant influence on UV254, divalent cation and monovalent cation rejections. The developed models revealed that interactions between feedwater composition and membrane properties impacted the rejection efficiency of membranes as significantly as water composition and membrane properties individually.

Bacteria↗
PubMed2004

Hindered gas-phase partitioning of trichloroethylene from aqueous cyclodextrin systems: implications for treatment and analysis.

Chemically enhanced flushing has shown great promise for attenuating subsurface nonaqueous phase liquid (NAPL) contamination. One particular chemically enhanced remediation technology is cyclodextrin enhanced flushing (CDEF). CDEF has been demonstrated as a viable alternative to conventional and innovative remediation methods. However, the presence of cyclodextrin (CD) in solution complicates the treatment and analysis of volatile organic compounds, such as trichloroethylene (TCE). The principal reason for the complications is the presence of TCE in three compartments instead of two, i.e., the aqueous solution, the vapor phase, and complexed inside the soluble CD molecule. Aqueous TCE-CD systems were examined at various concentration and temperature conditions and their respective Henry's law constants were measured. The presence of CD significantly decreased Henry's law constant of TCE. On the basis of these results, a quantitative model was developed to predict the additional effort that becomes necessary when air-stripping TCE from CDEF flushing solution. The modeling results demonstrate that the presence of CD requires significantly higher gas flow rates or longer residence times of the flushing solution inside an air stripper. Similarly, current gas chromatographic purge-and-trap methods for TCE analysis in CD solution appear to underestimate the aqueous phase TCE concentration if the CD concentration of the sample is not accounted for. Although this model was developed specifically for CD-TCE systems, it is likely that these results have implications for other VOCs and other solubilization enhancing agents, such as surfactants or cosolvents.

Cyclodextrins↗
PubMed2004

Theoretical study of the stereoselective additions of chiral alcohols to ketenes.

In 1989, Larsen et al. at Merck discovered that the addition of chiral alcohols to ketenes provided enantiomerically enriched aryl propionic acids, compounds valued for their therapeutic antiinflammatory properties. The high 1,4-asymmetric induction observed (>99:1 dr in the addition, and up to 99% ee after hydrolysis to the acid) is rare. A quantitative model based on B3LYP density functional theory calculations accounts for the stereoselectivity in the addition of (S)-methyl lactate, (S)-3-methyl-2-butanol, and (S)-pantolactone to methylphenylketene. The conformational processes of the intermediates can impact the stereoselectivity of the process, and either the addition step, or the protonation of the enolate intermediate, may be stereoselectivity determining.

Alcohols↗
PubMed2004

Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure.

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel beta-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel beta-sheet. In the proteins with antiparallel beta-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic "Z"-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.

Amides↗
PubMed2006

Importance of direct spin-spin coupling and spin-flip excitations for the zero-field splittings of transition metal complexes: a case study.

This work reports the evaluation of several theoretical approaches to the zero-field splitting (ZFS) in transition metal complexes. The experimentally well-known complex [Mn(acac)3] is taken as an example. The direct spin-spin contributions to the ZFS have been calculated on the basis of density functional theory (DFT) or complete active space self-consistent field (CASSCF) wave functions and have been found to be much more important than previously assumed. The contributions of the direct term may exceed approximately 1 cm(-1) in magnitude and therefore cannot be neglected in any treatment that aims at a realistic quantitative modeling of the ZFS. In the DFT framework, two different variants to treat the spin-orbit coupling (SOC) term have been evaluated. The first approach is based on previous work by Pederson, Khanna, and Kortus, and the second is based on a "quasi-restricted" DFT treatment which is rooted in our previous work on ZFS. Both approaches provide very similar results and underestimate the SOC contribution to the ZFS by a factor of 2 or more. The SOC is represented by an accurate multicenter spin-orbit mean-field (SOMF) approximation which is compared to the popular effective DFT potential-derived SOC operator. In addition to the DFT results, direct "infinite order" ab initio calculations of the SOC contribution to the ZFS based on CASSCF wave functions, the spectroscopy-oriented configuration interaction (SORCI), and the difference-dedicated CI (DDCI) approach are reported. In general, the multireference ab initio results provide a more realistic description of the ZFS in [Mn(acac)3]. The conclusions likely carry over to many other systems. This is attributed to the explicit treatment of the multiplet effects which are of dominant importance, since the calculations demonstrate that, even in the high-spin d4 system MnIII, the spin-flip excitations make the largest contribution to the SOC. It is demonstrated that the ab initio methods can be used even for somewhat larger molecules (the present calculations were done with more than 500 basis functions) in a reasonable time frame. Much more economical but still fairly reasonable results have been achieved with the INDO/S treatment based on CASSCF and SOC-CI wave functions.

Journal Article↗
PubMed1994

The use of the GRID program in the 3-D QSAR analysis of a series of calcium-channel agonists.

The use of GRID in the 3-D QSAR analysis of a series of calcium-channel agonists is described. Partial least-squares analysis of GRID maps showing the interaction energy between an alkyl hydroxyl probe and a series of agonists in 3-D space generated a predictive quantitative model of the variation of biological activity. The macroscopic descriptors CLOGP and CMR were included in the analysis, and the importance of appropriate block scaling is highlighted. The discussion highlights the interpretation of the resulting regression maps, and the steric, electrostatic, lipophilic, and hydrogen-bonding preferences of the calcium-channel receptor are identified.

Animals↗
PubMed1996

Structure-activity analysis of anandamide analogs: relationship to a cannabinoid pharmacophore.

Anandamides are endogenous fatty acid ethanolamides that have been shown to bind to the cannabinoid receptor and possess cannabimimetic activity yet are structurally dissimilar from the classical cannabinoids found in Cannabis sativa. We have employed molecular dynamics studies of a variety of anandamides to characterize their conformational mobility and determine whether there are pharmacophoric similarities with delta 9-THC. We have found that a looped conformation of these arachidonyl compounds is energetically favorable and that a structural correlation between this low-energy conformation and the classical cannabinoids can be obtained with the superposition of (1) the oxygen of the carboxyamide with the pyran oxygen in delta 9-THC, (2) the hydroxyl group of the ethanol with the phenolic hydroxyl group of delta 9-THC, (3) the five terminal carbons and the pentyl side chain of delta9-THC, and (4) the polyolefin loop overlaying with the cannabinoid tricyclic ring. The shape similarity is extended to show that other fatty acid ethanolamides that possess varying degrees of unsaturation also vary in their conformational mobility, which affects their ability to overlay with delta 9-THC as described above. Within this series of compounds, the most potent analog, the tetraene (arachidonyl) analog (i.e., anandamide itself), was determined to have restricted conformational mobility that favored an optimal pharmacophore overlay with delta9-THC. Eight pharmacologically active anandamide analogs are shown to have similar conformational mobility and pharmacophore alignments that are conformationally accessible. Furthermore, when these compounds are aligned to delta 9-THC according to the proposed pharmacophore overlay, their potencies are predicted by a quantitative model of cannabinoid structure--activity relationships based solely on classical and nonclassical cannabinoids with a reasonable degree of accuracy. The ability to incorporate the pharmacological potency of these anandamides into the cannabinoid pharmacophore model is also shown to support the relevance of the proposed pharmacophore model.

Animals↗
PubMed2000

A novel approach for the virtual screening and rational design of anticancer compounds.

A topological substructural approach to molecular design (TOSS-MODE) has been introduced for the selection and design of anticancer compounds. A quantitative model that discriminates anticancer compounds from the inactive ones in a training series was obtained. This model permits the correct classification of 91.43% of compounds in an external prediction set with only 1.43% of false actives and 7. 14% of false inactives. The model developed is then used in a simulation of a virtual search for Ras FTase inhibitors; 87% of the Ras FTase inhibitors used in this simulated search were correctly classified, thus indicating the ability of the TOSS-MODE model of finding lead compounds with novel structures and mechanism of action. Finally, a series of carbonucleosides was designed, and the compounds were classified as active/inactive anticancer compounds by using the model developed here. From the compounds so-designed, 20 were synthesized and evaluated experimentally for their antitumor effects on the proliferation of murine leukemia cells (L1210/0) and human T-lymphocyte cells (Molt4/C8 and CEM/0); 80% of these compounds were well-classified, as active or inactive, and only two pairs of isomeric compounds were false actives. The chloropurine derivatives were the most active compounds, especially compounds 6c, d.

Alkyl and Aryl Transferases↗
PubMed1997

Occurrence and Minimization of Cysteine Racemization during Stepwise Solid-Phase Peptide Synthesis(1)(,)(2).

Contrary to the conventional wisdom of the peptide synthesis field, N,S-protected derivatives of cysteine can undergo substantial levels of racemization with widely-used reagents and protocols for stepwise incorporation. A systematic study of this problem has been carried out as a function of coupling conditions and beta-thiol protecting groups, i.e., S-acetamidomethyl (Acm), S-triphenylmethyl (trityl or Trt), S-2,4,6-trimethoxybenzyl (Tmob), and S-9H-xanthen-9-yl (Xan), taking advantage of a convenient and quantitative model system assay involving HPLC resolution of H-Gly-L-Cys-Phe-NH(2) from H-Gly-D-Cys-Phe-NH(2). For example, standard protocols for couplings mediated by phosphonium and aminium salts, e.g., (benzotriazolyloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), N-[(1H-benzotriazol-1-yl)(dimethylamino)methylene]-N-methylmethanaminium hexafluorophosphate N-oxide (HBTU), N-[[(dimethylamino)-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl]methylene]-N-methylmethanaminium hexafluorophosphate N-oxide (HATU), and (7-azabenzotriazol-1-yloxy)tris(pyrrolidino)phosphonium hexafluorophosphate (PyAOP), typically involve 5-min preactivation times and are conducted in the presence of suitable additives such as 1-hydroxybenzotriazole (HOBt) or 7-aza-1-hydroxybenzotriazole (HOAt) plus a tertiary amine base such as N,N-diisopropylethylamine (DIEA) or N-methylmorpholine (NMM). Under such conditions, the levels of racemization in the model peptide, expressed as the ratio of D:L peptide formed, were in the entirely unacceptable range of 5-33%. However, these levels were in general reduced by a factor of 6- or 7-fold by avoiding the preactivation step. Additional strategies to reduce racemization involved change to a weaker base, with 2,4,6-trimethylpyridine (TMP, collidine) being substantially better than DIEA or NMM; 2-fold reduction in the amount of base; and change in solvent from neat N,N-dimethylformamide (DMF) to the less polar CH(2)Cl(2)-DMF (1:1). Coupling methods for the safe incorporation of cysteine with minimal racemization (<1% per step) in 9-fluorenylmethyloxycarbonyl (Fmoc) solid-phase peptide synthesis include BOP (or HBTU or HATU)/HOBt (or HOAt)/TMP (4:4:4) without preactivation in CH(2)Cl(2)-DMF (1:1), DIPCDI/HOBt (or HOAt) (4:4) with 5-min preactivation, and preformed pentafluorophenyl (Pfp) esters in CH(2)Cl(2)-DMF (1:1).

Journal Article↗
PubMed2005

Excited-state mixed valence in a diphenyl hydrazine cation: Spectroscopic consequences of coupling and transition dipole moment orientation.

A quantitative model of mixed-valence excited-state spectroscopy is developed and applied to 2,3-diphenyl-2,3-diazabicyclo[2.2.2]octane. The lowest-energy excited state of this molecule arises from a transition from the ground state, where the charge is located on the hydrazine bridge, to an excited state where the charge is associated with one phenyl group or the other. Coupling splits the absorption band into two components with the lower-energy component being the most intense. The sign of the coupling, derived by using a neighboring orbital model, is positive. The transition dipole moments consist of parallel and antiparallel vector components, and selection rules for each are derived. Bandwidths are caused by progressions in totally symmetric modes determined from resonance Raman spectroscopic analysis. The absorption, emission, and Raman spectra are fit simultaneously with one parameter set.

Cations↗
PubMed2005

Evaluation of Hofmeister effects on the kinetic stability of proteins.

Dissolved salts are known to affect properties of proteins in solution including solubility and melting temperature, and the effects of dissolved salts can be ranked qualitatively by the Hofmeister series. We seek a quantitative model to predict the effects of salts in the Hofmeister series on the deactivation kinetics of enzymes. Such a model would allow for a better prediction of useful biocatalyst lifetimes or an improved estimation of protein-based pharmaceutical shelf life. Here we consider a number of salt properties that are proposed indicators of Hofmeister effects in the literature as a means for predicting salt effects on the deactivation of horse liver alcohol dehydrogenase (HL-ADH), alpha-chymotrypsin, and monomeric red fluorescent protein (mRFP). We find that surface tension increments are not accurate predictors of salt effects but find a common trend between observed deactivation constants and B-viscosity coefficients of the Jones-Dole equation, which are indicative of ion hydration. This trend suggests that deactivation constants (log k(d,obs)) vary linearly with chaotropic B-viscosity coefficients but are relatively unchanged in kosmotropic solutions. The invariance with kosmotropic B-viscosity coefficients suggests the existence of a minimum deactivation constant for proteins. Differential scanning calorimetry is used to measure protein melting temperatures and thermodynamic parameters, which are used to calculate the intrinsic irreversible deactivation constant. We find that either the protein unfolding rate or the rate of intrinsic irreversible deactivation can control the observed deactivation rates.

Alcohol Dehydrogenase↗
PubMed2006

Study of rhamnose radicals in the solid state adopting a density functional theory cluster approach.

A theoretical study is performed on the radiation-induced radicals in crystalline alpha-l-rhamnose, using density functional theory (DFT) calculations. Irrespective of earlier structural assignments, a host of possible radical models is examined in search for a structure that accurately reproduces experimental electron paramagnetic resonance (EPR) properties. A cluster approach is followed, incorporating all hydrogen bond interactions between radical and crystalline environment. Hyperfine coupling tensors as well as g tensors are determined and a comparison is made with available experimental data. Three carbon-centered hydroxyalkyl radicals are validated, in accordance with experimental suggestions for their structure. The occurrence of a carbon-centered oxygen anion radical for one of the radical species is rejected on theoretical grounds, and instead an altered hydroxyalkyl structure is suggested. Our cluster calculations are able to determine g and hyperfine tensors for the oxygen-centered alkoxy radical in rhamnose, in accordance with one of the two measurements for this species. For all radical models, quantitative agreement with experimental hyperfine tensors is obtained by performing full cluster DFT calculations. The inclusion of the molecular environment for the determination of this EPR property proved to be essential.

Algorithms↗
PubMed2006

Charge delocalization in the special-pair radical cation of mutant reaction centers of Rhodobacter sphaeroides from Stark spectra and nonadiabatic spectral simulations.

Stark and absorption spectra for the hole-transfer band of the bacteriochlorophyll special pair in the wild-type and L131LH, M160LH, and L131LH/M160LH mutants of the bacterial reaction center of Rhodobacter sphaeroides are presented, along with extensive analyses based on nonadiabatic spectral simulations. Dramatic changes in the Stark spectra are induced by the mutations, changes that are readily interpreted in terms of the redox-energy asymmetry and degree of charge localization in the special-pair radical cation. The effect of mutagenesis on key properties such as the electronic coupling within the special pair and the reorganization energy associated with intervalence hole transfer are determined for the first time. Results for the L131LH and M160LH/L131LH mutants indicate that these species can be considered as influencing the special pair primarily through modulation of the redox asymmetry, as is usually conceptualized, but M160LH is shown to develop a wide range of effects that can be interpreted in terms of significant mutation-induced structural changes in and around the special pair. The nonadiabatic spectra simulations are performed using both a simple two-state 1-mode and an extensive four-state 70-mode model, which includes the descriptions of additional electronic states and explicitly treats the major vibrational modes involved. Excellent agreement between the two simulation approaches is obtained. The simple model is shown to reproduce key features of the Stark effect of the main intervalence transition, while the extensive model quantitatively reproduces most features of the observed spectra for both the electronic and the phase-phonon regions, thus giving a more comprehensive description of the effect of the mutations on the properties of the special-pair radical cation. These results for a series of closely related mixed-valence complexes show that the Stark spectra provide a sensitive indicator for the properties of the mixed-valence complexes and should serve as an instructive example on the application of nonadiabatic simulations to the study of mixed-valence complexes in general as well as other chemical systems akin to the photosynthetic special pair.

Absorption↗
PubMed2004

Adsorption of ionic surfactants at an expanding air-water interface.

A quantitative model for the kinetics of adsorption of ionic surfactants to an expanding liquid surface is presented for surfactant concentrations below and above the critical micelle concentration (cmc). For surfactant concentrations below the cmc, the electrostatic double layer is accounted for explicitly in the adsorption isotherm. An overflowing cylinder (OFC) was used to create nonequilibrium liquid surfaces under steady-state conditions. Experimental measurements of the surface excess for solutions of cationic surfactants CH3(CH2)n-1N+(CH3)3 Br- (CnTAB, n = 12, 14, 16) and the anionic fluorocarbon surfactant sodium bis(1H,1H-nonafluoropentyl)-2-sulfosuccinate (di-CF4) in the OFC are in excellent agreement with the theoretical predictions for diffusion-controlled adsorption for all concentrations studied below the cmc. For surfactant concentrations above cmc, the diffusion ofmicelles and monomers are handled separately under the assumption of fast micellar breakdown. This simplified model gives excellent agreement for the system C14TAB + 0.1 M NaBr above the cmc. Agreement between theory and experiment for C16TAB + 0.1 M NaBr is less good. A plausible explanation for the discrepancy is that micellar breakdown is no longer fast on the time scale of the OFC (ca. 0.1 s).

Journal Article↗
PubMed2005

Wetting and wetting transitions on copper-based super-hydrophobic surfaces.

Rough and patterned copper surfaces were produced using etching and, separately, using electrodeposition. In both of these approaches the roughness can be varied in a controlled manner and, when hydrophobized, these surfaces show contact angles that increase with increasing roughness to above 160 degrees . We show transitions from a Wenzel mode, whereby the liquid follows the contours of the copper surface, to a Cassie-Baxter mode, whereby the liquid bridges between features on the surface. Measured contact angles on etched samples could be modeled quantitatively to within a few degrees by the Wenzel and Cassie-Baxter equations. The contact angle hysteresis on these surfaces initially increased and then decreased as the contact angle increased. The maximum occurred at a surface area where the equilibrium contact angle would suggest that a substantial proportion of the surface area was bridged.

Journal Article↗