Gibbs Energy of Superoxide Dismutase Heterodimerization Accounts for Variable Survival in Amyotrophic Lateral Sclerosis.

The exchange of subunits between homodimeric mutant Cu, Zn superoxide dismutase (SOD1) and wild-type (WT) SOD1 is suspected to be a crucial step in the onset and progression of amyotrophic lateral sclerosis (ALS). The rate, mechanism, and ΔG of heterodimerization (ΔGHet) all remain undetermined, due to analytical challenges in measuring heterodimerization. This study used capillary zone electrophoresis to measure rates of heterodimerization and ΔGHet for seven ALS-variant apo-SOD1 proteins that are clinically diverse, producing mean survival times between 2 and 12 years (postdiagnosis). The ΔGHet of each ALS variant SOD1 correlated with patient survival time after diagnosis (R(2) = 0.98), with more favorable ΔGHet correlating with shorter survival by 4.8 years per kJ. Rates of heterodimerization did not correlate with survival time or age of disease onset. Metalation diminished the rate of subunit exchange by up to ∼38-fold but only altered ΔGHet by <1 kJ mol(-1). Medicinal targeting of heterodimer thermodynamics represents a plausible strategy for prolonging life in SOD1-linked ALS.

Accumulation and depuration of trinitrotoluene and related extractable and nonextractable (bound) residues in marine fish and mussels.

To determine if trinitrotoluene (TNT) forms nonextractable residues in mussels (Mytilus galloprovincialis) and fish (Cyprinodon variegatus) and to measure the relative degree of accumulation as compared to extractable TNT and its major metabolites, organisms were exposed to water fortified with (14)C-TNT. After 24 h, nonextractable residues made up 75% (mussel) and 83% (fish) while TNT accounted for 2% of total radioactivity. Depuration half-lives for extractable TNT, aminodinitrotoluenes (ADNTs) and diaminonitrotoluenes (DANTs) were fast initially (<0.5 h), but slower for nonextractable residues. Nonextractable residues from organisms were identified as ADNTs and DANTs using 0.1 M HCL for solubilization followed by liquid chromatography-tandem mass spectrometry. Recovered metabolites only accounted for a small fraction of the bound residue quantified using a radiotracer likely because of low extraction or hydrolysis efficiency or alternative pathways of incorporation of radiolabel into tissue.

Metal-ion-specific screening of charge effects in protein amide H/D exchange and the Hofmeister series.

In this study, protein charge ladders and mass spectrometry were used to quantify how metal cations in the Hofmeister series (Na(+), K(+), Li(+), Mg(2+), and Ca(2+)) permute the effects of lysine acetylation on the rate of amide H/D exchange in a representative protein (myoglobin, Mb). The successive acetylation of up to 18 Lys-ε-NH3(+) groups in Mb caused a linear decrease in its global rate of amide H/D exchange (as measured by mass spectrometry), despite also decreasing the thermostability of Mb by >10 °C. The ability of a metal cation to screen kinetic electrostatic effects during H/D exchange-and to abolish the protective effect of acetylation against H/D exchange-was found to depend on the position of the cation in the Hofmeister series. Na(+) and K(+) cations did not fully equalize the rates of H/D exchange among each "rung" of the charge ladder, whereas Mg(2+) and Ca(2+) did equalize rates without eliminating the hydrophobic core of the protein (i.e., without unfolding Mb); Li(+) exhibited intermediate effects. The ability of Mg(2+) and Ca(2+) to completely screen electrostatic effects associated with the H/D exchange of charge isomers of Mb suggests that Mg(2+) or Ca(2+) (but not Na(+) or K(+)) can be used to quantify the magnitude by which electrostatic charge contributes to the observed rates of amide H/D exchange in proteins.

Effect of metal loading and subcellular pH on net charge of superoxide dismutase-1.

The net charge of a folded protein is hypothesized to influence myriad biochemical processes (e.g., protein misfolding, electron transfer, molecular recognition); however, few tools exist for measuring net charge and this elusive property remains undetermined--at any pH--for nearly all proteins. This study used lysine-acetyl "protein charge ladders" and capillary electrophoresis to measure the net charge of superoxide dismutase-1 (SOD1)--whose aggregation causes amyotrophic lateral sclerosis (ALS)--as a function of coordinated metal ions and pH. The net negative charge of apo-SOD1 was similar to predicted values; however, the binding of a single Zn(2+) or Cu(2+) ion reduced the net negative charge by a greater magnitude than predicted (i.e., ~4 units, instead of 2), whereas the SOD1 protein underwent charge regulation upon binding 2-4 metal ions. From pH5 to pH8 (i.e., a range consistent with the multiple subcellular loci of SOD1), the holo-SOD1 protein underwent smaller fluctuations in net negative charge than predicted (i.e., ~3 units, instead of ~14) and did not undergo charge inversion at its isoelectric point (pI=5.3) but remained anionic. The regulation of SOD1 net charge along its pathways of metal binding, and across solvent pH, provides insight into its metal-induced maturation and enzymatic activity (which remains diffusion-limited across pH5-8). The anionic nature of holo-SOD1 across subcellular pH suggests that ~45 different ALS-linked mutations to SOD1 will reduce its net negative charge regardless of subcellular localization.

Ligand-induced protein mobility in complexes of carbonic anhydrase II and benzenesulfonamides with oligoglycine chains.

This paper describes a biophysical investigation of residual mobility in complexes of bovine carbonic anhydrase II (BCA) and para-substituted benzenesulfonamide ligands with chains of 1-5 glycine subunits, and explains the previously observed increase in entropy of binding with chain length. The reported results represent the first experimental demonstration that BCA is not the rigid, static globulin that has been typically assumed, but experiences structural fluctuations upon binding ligands. NMR studies with (15)N-labeled ligands demonstrated that the first glycine subunit of the chain binds without stabilization or destabilization by the more distal subunits, and suggested that the other glycine subunits of the chain behave similarly. These data suggest that a model based on ligand mobility in the complex cannot explain the thermodynamic data. Hydrogen/deuterium exchange studies provided a global estimate of protein mobility and revealed that the number of exchanged hydrogens of BCA was higher when the protein was bound to a ligand with five glycine subunits than when bound to a ligand with only one subunit, and suggested a trend of increasing number of exchanged hydrogens with increasing chain length of the BCA-bound ligand, across the series. These data support the idea that the glycine chain destabilizes the structure of BCA in a length-dependent manner, causing an increase in BCA mobility. This study highlights the need to consider ligand-induced mobility of even "static" proteins in studies of protein-ligand binding, including rational ligand design approaches.

Abnormal SDS-PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding.

The amino acid substitution or post-translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS-PAGE. This type of "gel shifting" has perplexed biochemists and biologists for decades. We identify a mechanism for "gel shifting" that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post-translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS-PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues ~80-101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80-101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demonstrated that amino acid substitutions increase migration during SDS-PAGE by promoting the binding of three to four additional SDS molecules, without significantly altering the secondary structure or Stokes radius of hSOD1-SDS complexes. The high negative charge of domain 80-101 is required for SOD1 gel shifting: neutralizing the polyacidic domain (via chimeric mouse-human SOD1 fusion proteins) inhibited amino acid substitutions from causing gel shifting. These results demonstrate that the pattern of gel shifting for mutant cytosolic proteins can be used to: (i) identify domains in the primary structure that control interactions between denatured cytosolic proteins and SDS and (ii) identify a predominant chemical mechanism for the interaction (e.g., hydrophobic vs. electrostatic).

Rapid analysis of carbohydrates in aqueous extracts and hydrolysates of biomass using a carbonate-modified anion-exchange column.

Quantitative liquid-chromatography techniques used to characterize carbohydrates present in biomass samples can suffer from long analysis times, limited analyte resolution, poor stability, or a combination of these factors. The current manuscript details a novel procedure enabling resolution of glucose, xylose, arabinose, galactose, mannose, fructose, and sucrose via isocratic elution in less than 5 min. Equivalent conditions also enable analysis of cellobiose and maltose with a minimal increase in chromatographic run time (ca. 3 and 6 min, respectively). Noted chromatographic performance requires that a commercially available anion-exchange column be modified with carbonate prior to analysis. Analytical performance of a modified column was assessed over a 5-day period via repeated analyses of 4 samples, resulting from aqueous extraction or quantitative saccharification of a potential biofuel feedstock (i.e., corn stover or switchgrass). A simple solid phase extraction procedure was utilized to clean up each sample prior to analysis. Analytical accuracy of the extraction protocol was assessed by evaluation of matrix spike recoveries which typically ranged from 84% to 98%. The instrumental variability of measured concentrations in real samples over the 5-day period was generally less than 5% RSD for all detected analytes, independent of sample type. Finally, it is important to note that the modified column exhibited exceptional stability over approximately 800 injections of biofeedstock-based samples. These data demonstrate that a carbonate-modified anion-exchange column can be employed for rapid determination of carbohydrates in biomass samples of lignocellulosic origin.

Effect of varying feedstock-pretreatment chemistry combinations on the formation and accumulation of potentially inhibitory degradation products in biomass hydrolysates.

A variety of potentially inhibitory degradation products are produced during pretreatment of lignocellulosic biomass. Qualitative and quantitative interrogation of pretreatment hydrolysates is paramount to identifying potential correlations between pretreatment chemistries and microbial inhibition in downstream bioconversion processes. In the present study, corn stover, poplar, and pine feedstocks were pretreated under eight different chemical conditions, which are representative of leading pretreatment processes. Pretreatment processes included: 0.7% H(2)SO(4), 0.07% H(2)SO(4), liquid hot water, neutral buffer solution, aqueous ammonia, lime, lime with oxygen pressurization, and wet oxidation. Forty lignocellulosic degradation products resulting from pretreatment were analyzed using high performance liquid chromatography in combination with UV spectroscopy or tandem mass spectrometry detection (HPLC-PDA-MS/MS) and ion chromatography (IC). Of these compounds, several have been reported to be inhibitory, including furfural, hydroxymethyl furfural, ferulic acid, 3,4-dihydroxybenzaldehyde, syringic acid among others. Formation and accumulation of monitored compounds in hydrolysates is demonstrated to be a function of both the feedstock and pretreatment conditions utilized.

Compositional analysis of water-soluble materials in switchgrass.

Any valuation of a potential feedstock for bioprocessing is inherently dependent upon detailed knowledge of its chemical composition. Accepted analytical procedures for compositional analysis of biomass water-soluble extracts currently enable near-quantitative mass closure on a dry weight basis. Techniques developed in conjunction with a previous analytical assessment of corn stover have been applied to assess the composition of water-soluble materials in four representative switchgrass samples. To date, analytical characterization of water-soluble material in switchgrass has resulted in >78% mass closures for all four switchgrass samples, three of which have a mass closure of >85%. Over 30 previously unknown constituents in aqueous extracts of switchgrass were identified and quantified using a variety of chromatographic techniques. Carbohydrates (primarily sucrose, glucose, and fructose) were found to be the predominant water-soluble components of switchgrass, accounting for 18-27% of the dry weight of extractives. Total glycans (monomeric and oligomeric sugars) contributed 25-32% to the dry weight of extractives. Additional constituents contributing to the mass balance for extractives included various alditols (2-3%), organic acids (10-13%), inorganic ions (11-13%), and a distribution of oligomers presumed to represent a diverse mixture of lignin-carbohydrate complexes (30-35%). Switchgrass results are compared with previous analyses of corn stover extracts and presented in the context of their potential impact on biomass processing, feedstock storage, and future analyses of feedstock composition.

Compositional analysis of water-soluble materials in corn stover.

Corn stover is one of the leading feedstock candidates for commodity-scale biomass-to-ethanol processing. The composition of water-soluble materials in corn stover has been determined with greater than 90% mass closure in four of five representative samples. The mass percentage of water-soluble materials in tested stover samples varied from 14 to 27% on a dry weight basis. Over 30 previously unknown constituents of aqueous extracts were identified and quantified using a variety of chromatographic techniques. Monomeric sugars (primarily glucose and fructose) were found to be the predominant water-soluble components of corn stover, accounting for 30-46% of the dry weight of extractives (4-12% of the dry weight of feedstocks). Additional constituents contributing to the mass balance for extractives included various alditols (3-7%), aliphatic acids (7-21%), inorganic ions (10-18%), oligomeric sugars (4-12%), and a distribution of oligomers tentatively identified as being derived from phenolic glycosides (10-18%).

Pseudo reaction kinetics of organic degradation products in dilute-acid-catalyzed corn stover pretreatment hydrolysates.

A variety of degradation products are produced upon pretreatment of lignocellulosic biomass with dilute acid. To date, the complexity of these samples has significantly limited the scope of efforts to perform summative analyses of degradation products. Qualitative and quantitative interrogation of hydrolysates is also paramount to identifying potential correlations between pretreatment chemistry and microbial inhibition in downstream bioconversion processes. A recently developed reversed-phase high performance liquid chromatography technique with UV detection has been applied to perform quantitative assessments of a variety of hydrolysate components as a function of pretreatment time and temperature. Correlations of product concentrations to the pretreatment severity function indicate differing responses of various compounds to the kinetic influences of temperature and reaction time. Of the compounds measured, four demonstrated initial accumulation rates were sufficiently linear over the time period tested to enable determination of activation energy E(a). All four compounds appear to demonstrate higher E(a) than that assumed in the commonly applied severity function. Overall accumulation trends for most compounds indicated similar under-estimation of apparent activation energy by the severity function. Biotechnol. Bioeng. 2007;98: 1135-1145. (c) 2007 Wiley Periodicals, Inc.

High-performance liquid chromatography method for simultaneous determination of aliphatic acid, aromatic acid and neutral degradation products in biomass pretreatment hydrolysates.

A variety of degradation products are produced upon dilute acid pretreatment of lignocellulosic biomass. Within this larger construct, organic acids, phenols and aromatic aldehydes represent important compound classes to investigate due to increasing evidence of their inhibitory effect on fermentative microorganisms. An analytical extraction procedure is presented, enabling isolation of potential analytes away from alternative products in biomass hydrolysates. Additionally, a reversed-phase high-performance liquid chromatography (HPLC) method has been developed and validated, affording simultaneous separation and quantitative determination of 32 potential analytes in water with UV detection at 210 nm. The method was subsequently employed to quantify a variety of aliphatic acid, aromatic acid, aldehyde and phenolic degradation products in a corn-stover hydrolysate at concentration levels ranging from 0.02 to 41 mM.

Photochemical tissue bonding using monomeric 4-amino-1,8-naphthalimides.

Certain substituted naphthalimides have been shown to produce, on photochemical activation, mechanically viable bonds between a variety of tissue surfaces. It is believed that these compounds act as photochemically activated oxidants, catalyzing the formation of reactive intermediates in the extracellular matrices of approximated tissue surfaces. The condensation of these intermediates results in the formation of crosslinks between the intimate surfaces. Of particular interest is the application of this technique to the repair of tears in the typically unrepairable avascular zone of menisci. The menisci are collagen-rich fibrocartilaginous tissues that support up to 90% of the load across the knee joint and participate in important functions including shock absorption, joint stabilization, hyperextension prevention, and lubrication of the knee. Preliminary ex vivo and in vivo work in our laboratories has demonstrated that photochemically activated naphthalimides have significant potential for the repair of meniscal lesions. We describe preliminary ex vivo studies assessing the relative abilities of a variety of water-soluble monomeric 4-amino-1,8-naphthalimides to bond bovine knee meniscal tissue on visible light irradiation.