Biomedical subjects

James R Lepock

Publications and source records attributed to James R Lepock.

16 recordsLinked to original sources

PubMed2006

Equilibrium thermodynamic analysis of amyotrophic lateral sclerosis-associated mutant apo Cu,Zn superoxide dismutases.

The folding and thermodynamic properties of metal free (apo) superoxide dismutases (SODs) are systematically analyzed using equilibrium guanidinium chloride (GdmCl) curves and differential scanning calorimetry (DSC). Chemically and structurally diverse amyotrophic lateral sclerosis (ALS)-associated mutations (G85R, G93R, E100G, I113T) are introduced into a pseudo-wild-type background that has no free cysteines, resulting in highly reversible unfolding. Analysis of the protein concentration dependence of GdmCl curves reveals formation of a monomer intermediate in equilibrium with native dimer and unfolded monomer. Global fitting of the data enables quantitative measurement of free energy changes for both dimer dissociation and monomer intermediate stability. All the mutations decrease protein stability, mainly by destabilizing the monomer intermediate, but also by tending to weaken dimerization, even for mutations far from the dimer interface. Thus, the effects of mutations seem to propagate through the apo protein, and result in increased population of both intermediate and unfolded monomers. This may underlie increased formation of toxic aggregates by mutants in ALS. Analysis of DSC data for apo SODs is consistent with stability measurements from GdmCl curves and provides further evidence for increased aggregation by mutant proteins through increased ratios of van't Hoff to calorimetric enthalpies of unfolding.

Calorimetry, Differential Scanning↗

PubMed2006

Calorimetric analysis of thermodynamic stability and aggregation for apo and holo amyotrophic lateral sclerosis-associated Gly-93 mutants of superoxide dismutase.

Differential scanning calorimetry was used to measure changes in thermodynamic stability and aggregation for glycine 93 mutants of human copper, zinc-superoxide dismutase (SOD). Glycine 93 is a conserved residue at position i + 3 of a tight turn and has been found to be a mutational hot spot in familial amyotrophic lateral sclerosis (fALS). The fALS-associated mutations, G93A, G93S, G93R, G93D, and G93V, were made in a pseudo wild-type background containing no free cysteines, which prevented the formation of aberrant disulfide bonds upon thermal unfolding, and enabled quantitative thermodynamic analysis of the effects of the mutations. Thermal unfolding was highly reversible for all the SODs in both the fully metallated (holo) and metal-free (apo) forms. The data for all the holo-SODs and for the apo-pseudo-wild-type SOD were well fit by a 2-state unfolding model for native dimer (N2) to two unfolded monomers (2U), N2 <--> 2U. The holo- and apo-forms of the mutants are significantly destabilized (by 1.5-3.5 kcal mol(-1) monomer) relative to the corresponding forms of pseudo wild-type, with the relative stabilities being correlated with statistical preferences for amino acids in this structural context. Although van't Hoff (DeltaHvH) to calorimetric (DeltaHcal) enthalpy ratios are close to unity for all the holo-SODs and for apo-pseudo-wild-type, consistent with a 2-state transition, DeltaHvH is considerably larger than DeltaHcal for all the apo-mutants. This suggests that the mutations cause apo-SOD to have an increased propensity to misfold or aggregate, which may be linked to increased toxic mutant SOD aggregation in fALS.

Amino Acid Substitution↗

PubMed2005

Mechanism and thermodynamics of guanidinium chloride-induced denaturation of ALS-associated mutant Cu,Zn superoxide dismutases.

Mutations in human copper zinc superoxide dismutase (hSOD) that are associated with amyotrophic lateral sclerosis (ALS) have been proposed to destabilize the protein and thereby enhance toxic protein aggregation. In previous studies, denaturation of metallated (holo) hSODs was found to be irreversible, and complicated by the formation of intermolecular disulfide bonds. Here, ALS-associated mutations (E100G, G93A, G85R and A4V) are introduced into a pseudo wild-type background containing no free cysteine residues. The guanidinium chloride-induced denaturation of the holo proteins is generally found to be highly reversible (except for A4V, which tended to aggregate), enabling quantitative analysis of the effects of the mutations on protein stability. Denaturation and renaturation curves were monitored by tryptophan fluorescence, circular dichroism, enzyme activity, chemical cross-linking and analytical sedimentation, as a function of equilibration time and protein concentration. There is strong kinetic hysteresis, with curves requiring exceptionally long times (many days for pseudo wild-type) to reach equilibrium, and evidence for the formation of kinetic and equilibrium intermediate(s), which are more highly populated at lower protein concentrations. The effects of metal dissociation were included in the data fitting. The full protein concentration dependence is best described using a three-state model involving metallated native dimer, metallated monomeric intermediate and unfolded monomers with no bound metals; however, at high protein concentrations the unfolding approaches a two-state transition with metal binding to both the native dimers and unfolded monomers. We show that the E100G, G93A and G85R mutations decrease overall protein stability, largely by decreasing monomer stability with little effect on dimer dissociation. Comparison of the chemical denaturation data with ALS disease characteristics suggests that aggregation of some mutant hSOD may occur through increased population of partially folded states that are less stable than the monomeric intermediate and accessed from the destabilized holo protein.

Amyotrophic Lateral Sclerosis↗

PubMed2005

How do cells respond to their thermal environment?

Changes in growth temperature induce both activating and inactivating responses from cells, with the magnitude of the temperature change being among the factors that influence which type of response dominates. Aside from upregulated enzyme activity, induction of thermotolerance is the most widely studied and best understood activating response that cells exhibit following heat shock. Inactivating responses to heat shock that are of biomedical interest include heat radiosensitization and cytotoxicity. Interestingly, the activation energy for inducing thermotolerance, heat cytotoxicity, and radiosensitization all fall within a similar range of 120-146 kcal per mole. The relatively high activation energy for each of these responses suggests that they all involve a heat-induced molecular transition as a trigger, and several lines of research suggest strongly that protein denaturation is the common transition that triggers all three responses. Low levels of protein denaturation are sufficient to attract the 90 kDa heat shock protein (HSP90) such that it frees up heat shock factor 1, which then trimerizes to form an active transcription factor that upregulates expression of heat shock proteins. Upregulation of heat shock proteins and other heat-induced events result in the development of thermotolerance, which protects cells from subsequent exposure to heat shock and other stresses. A more severe heat shock increases protein denaturation proportionately and leads to aggregation of both denatured and native proteins. This results in inactivation of protein synthesis, cell cycle progression, and DNA repair processes such that cells either die or are sensitized to radiation and other cytotoxic events. The ultimate fate of cells following a heat shock depends upon the summation of the activation and inactivation events that are induced, which appears to be governed by the resultant magnitude of protein denaturation and aggregation. Treatments that stabilize cellular proteins against denaturation and aggregation reduce the magnitude of inactivating responses while increasing that of activating responses for a given heat shock (time at temperature), while treatments that sensitize proteins to denaturation and aggreation have the converse effect. These findings support the conclusion that the determinant of the cellular response to heat shock is the amount of heat-induced protein denaturation and aggregation and not the time at temperature.

Animals↗

PubMed2004

Measurement of protein stability and protein denaturation in cells using differential scanning calorimetry.

Many methods exist for measuring and studying protein denaturation in vitro. However, measuring protein denaturation in cells under conditions relevant to heat shock presents problems due to cellular complexity and high levels of light scattering that interfere with optical techniques. A general method for measuring protein denaturation in cells using high sensitivity differential scanning calorimetry (DSC) is given. Profiles of specific heat (c(p) vs. temperature) are obtained providing information about transitions in cellular components including the denaturation of proteins. The specific approaches employed with erythrocytes, bacteria, and mammalian cells are described, and an identification of several features of the DSC profiles is given. Protein denaturation on the level of roughly 7-20% occurs for commonly used heat shocks in mammalian cells.

Animals↗

PubMed2004

Sonication of proteins causes formation of aggregates that resemble amyloid.

Despite the widespread use of sonication in medicine, industry, and research, the effects of sonication on proteins remain poorly characterized. We report that sonication of a range of structurally diverse proteins results in the formation of aggregates that have similarities to amyloid aggregates. The formation of amyloid is associated with, and has been implicated in, causing of a wide range of protein conformational disorders including Alzheimer's disease, Huntington's disease, Parkinson's disease, and prion diseases. The aggregates cause large enhancements in fluorescence of the dye thioflavin T, exhibit green-gold birefringence upon binding the dye Congo red, and cause a red-shift in the absorbance spectrum of Congo red. In addition, circular dichroism reveals that sonication-induced aggregates have high beta-content, and proteins with significant native alpha-helical structure show increased beta-structure in the aggregates. Ultrastructural analysis by electron microscopy reveals a range of morphologies for the sonication-induced aggregates, including fibrils with diameters of 5-20 nm. The addition of preformed aggregates to unsonicated protein solutions results in accelerated and enhanced formation of additional aggregates upon heating. The dye-binding and structural characteristics, as well as the ability of the sonication-induced aggregates to seed the formation of new aggregates are all similar to the properties of amyloid. These results have important implications for the use of sonication in food, biotechnological and medical applications, and for research on protein aggregation and conformational disorders.

Amyloid↗

PubMed2004

HSP70 binds to the fast-twitch skeletal muscle sarco(endo)plasmic reticulum Ca2+ -ATPase (SERCA1a) and prevents thermal inactivation.

This study examined whether HSP70 could bind to and protect against thermal inactivation of SERCA1a, the SERCA isoform expressed in adult fast-twitch skeletal muscle. Sarcoplasmic reticulum vesicles prepared from rat gastrocnemius muscle were incubated with purified HSP70 at both 37 and 41 degrees C for either 30, 60, or 120 min. Maximal SERCA1a activity (micromol/g protein/min) in the absence of HSP70 was reduced progressively with time, with greater reductions occurring at 41 degrees C compared with 37 degrees C. HSP70 protected against thermal inactivation of SERCA1a activity at 37 degrees C but not at 41 degrees C and only at 30 and 60 min but not at 120 min. HSP70 also protected against reductions in binding capacity for fluorescein isothiocyanate, a fluorescent probe that binds to Lys515 in the nucleotide binding domain of SERCA, at 30 and 60 min but not at 120 min, an effect that was independent of temperature. HEK-293 cells were co-transfected with cDNAs encoding rabbit SERCA1a and human HSP-EYFP and subjected to 40 degrees C for 1 h. Immunohistochemistry revealed nearly complete co-localization of SERCA1a with HSP70 under these conditions. Co-immunoprecipitation showed physical interaction between HSP70 and SERCA1a under all thermal conditions both in vitro and in HEK-293 cells. Modeling showed that the fluorescein isothiocyanate-binding site of intact SERCA1a in the E2 form lies in its close proximity to a potential interaction site between SERCA1a and HSP70. These results indicate that HSP70 can bind to SERCA1a and, depending on the severity of heat stress, protect SERCA1a function by stabilizing the nucleotide binding domain.

Animals↗

PubMed2004

Role of hydrogen bonding in the active site of human manganese superoxide dismutase.

The side chain of Gln143, a conserved residue in manganese superoxide dismutase (MnSOD), forms a hydrogen bond with the manganese-bound solvent and is critical in maintaining catalytic activity. The side chains of Tyr34 and Trp123 form hydrogen bonds with the carboxamide of Gln143. We have replaced Tyr34 and Trp123 with Phe in single and double mutants of human MnSOD and measured their catalytic activity by stopped-flow spectrophotometry and pulse radiolysis. The replacements of these side chains inhibited steps in the catalysis as much as 50-fold; in addition, they altered the gating between catalysis and formation of a peroxide complex to yield a more product-inhibited enzyme. The replacement of both Tyr34 and Trp123 in a double mutant showed that these two residues interact cooperatively in maintaining catalytic activity. The crystal structure of Y34F/W123F human MnSOD at 1.95 A resolution suggests that this effect is not related to a conformational change in the side chain of Gln143, which does not change orientation in Y34F/W123F, but rather to more subtle electronic effects due to the loss of hydrogen bonding to the carboxamide side chain of Gln143. Wild-type MnSOD containing Trp123 and Tyr34 has approximately the same thermal stability compared with mutants containing Phe at these positions, suggesting the hydrogen bonds formed by these residues have functional rather than structural roles.

Binding Sites↗

PubMed2004

Monomeric Cu,Zn-superoxide dismutase is a common misfolding intermediate in the oxidation models of sporadic and familial amyotrophic lateral sclerosis.

Proteinacious intracellular aggregates in motor neurons are a key feature of both sporadic and familial amyotrophic lateral sclerosis (ALS). These inclusion bodies are often immunoreactive for Cu,Zn-superoxide dismutase (SOD1) and are implicated in the pathology of ALS. On the basis of this and a similar clinical presentation of symptoms in the familial (fALS) and sporadic forms of ALS, we sought to investigate the possibility that there exists a common disease-related aggregation pathway for fALS-associated mutant SODs and wild type SOD1. We have previously shown that oxidation of fALS-associated mutant SODs produces aggregates that have the same morphological, structural, and tinctorial features as those found in SOD1 inclusion bodies in ALS. Here, we show that oxidative damage of wild type SOD at physiological concentrations ( approximately 40 microm) results in destabilization and aggregation in vitro. Oxidation of either mutant or wild type SOD1 causes the enzyme to dissociate to monomers prior to aggregation. Only small changes in secondary and tertiary structure are associated with monomer formation. These results indicate a common aggregation prone monomeric intermediate for wild type and fALS-associated mutant SODs and provides a link between sporadic and familial ALS.

Amyotrophic Lateral Sclerosis↗

PubMed2003

Amino acid substitution at the dimeric interface of human manganese superoxide dismutase.

The side chains of His30 and Tyr166 from adjacent subunits in the homotetramer human manganese superoxide dismutase (Mn-SOD) form a hydrogen bond across the dimer interface and participate in a hydrogen-bonded network that extends to the active site. Compared with wild-type Mn-SOD, the site-specific mutants H30N, Y166F, and the corresponding double mutant showed 10-fold decreases in steady-state constants for catalysis measured by pulse radiolysis. The observation of no additional effect upon the second mutation is an example of cooperatively interacting residues. A similar effect was observed in the thermal stability of these enzymes; the double mutant did not reduce the major unfolding transition to an extent greater than either single mutant. The crystal structures of these site-specific mutants each have unique conformational changes, but each has lost the hydrogen bond across the dimer interface, which results in a decrease in catalysis. These same mutations caused an enhancement of the dissociation of the product-inhibited complex. That is, His30 and Tyr166 in wild-type Mn-SOD act to prolong the lifetime of the inhibited complex. This would have a selective advantage in blocking a cellular overproduction of toxic H2O2.

Amino Acids↗

PubMed2003

Molecular dynamics simulations of a protein model in uniform and elongational flows.

We present a molecular dynamics study of the conformational deformation of a minimalist beta-barrel protein model in two different types of hydrodynamic flows: uniform and elongational. We investigate the characteristics of protein stretching, paying special attention to the unfolding intermediate states and their relationship to the protein folding/unfolding problem. In the uniform flow simulations, one end of the modeled protein was tethered to a fixed point in space and the forced unfolding process was observed. The unfolding takes place via a few stages involving one or two intermediate states, depending on which end is tethered. The calculated force-extension curves show plateau regimes and hysteresis as the protein is stretched and refolded, in qualitative agreement with the experimental measurements. The physical behavior observed in our numerical simulations of the forced unfolding in an elongational flow is very different from that in uniform flow. The protein unfolds abruptly from the globular state to a fully stretched state without going through any observable intermediate states. From these observation, we stress that protein unfolding pathways under the influence of an external force are highly dependent on the mechanism of the exerted force.

Computer Simulation↗

PubMed2003

Minimal model for studying prion-like folding pathways.

The Monte Carlo technique is used to simulate the energy landscape and the folding kinetics of a minimal prion-like protein model. We show that the competition between hydrogen-bonding and hydrophobic interactions yields two energetically favored secondary structures, an alpha-helix and a beta-hairpin. Folding simulations indicate that the probability of reaching the alpha-helix form from a denatured random conformation is much higher than the probability of reaching the beta-sheet form, even though the beta-sheet has a lower energy. The existence of a lower energy beta-sheet state gives the possibility for the normal alpha-helix structure to take a structural transformation into the beta-sheet structure under external influences.

Hydrogen Bonding↗

PubMed2003

Unfolding proteins in an external field: can we always observe the intermediate states?

A protein molecule under the stress of an external denaturing force acting on a terminal end or on the entire molecule is expected to unfold, possibly through a few intermediate stages depending on the magnitude of the denaturing force. We have investigated two protein minimal models under various types of denaturing force fields using the collision molecular-dynamics simulation, in order to critically examine the relationship between the folding pathways observed in different protein denaturing experiments.

Biophysical Phenomena↗

PubMed2002

Recombinant lysine:N(6)-hydroxylase: effect of cysteine-->alanine replacements on structural integrity and catalytic competence.

Recombinant lysine:N(6)-hydroxylase, rIucD, catalyzes the hydroxylation of L-lysine to its N(6)-hydroxy derivative, with NADPH and FAD serving as cofactors in the reaction. The five cysteine residues present in rIucD can be replaced, individually or in combination, with alanine without effecting a major change in the thermal stability, the affinity for L-lysine and FAD, as well as the k(cat) for mono-oxygenase activity of the protein. However, when the susceptibility to modification by either 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) or 2,6-dichlorophenol indophenol (DPIP) serves as the criterion for monitoring conformational change(s) in rIucD and its muteins, Cys146-->Ala and Cys166-->Ala substitutions are found to induce an enhancement in the reactivity of one of the protein's remaining cysteine residues with concomitant diminution of mono-oxygenase function. In addition, the systematic study of cysteine-->alanine replacement has led to the identification of rIucD's Cys166 as the exposed residue which is detectable during the reaction of the protein with DTNB but not with iodoacetate. Substitution of Cys51 of rIucD with alanine results in an increase in mono-oxygenase activity (approx. 2-fold). Such replacement, unlike those of other cysteine residues, also enables the covalent DPIP conjugate of the protein to accommodate FAD in its catalytic function. A possible role of rIucD's Cys51 in the modulation of its mono-oxygenase function is discussed.

Alanine↗

PubMedDate not supplied

Cellular effects of hyperthermia: relevance to the minimum dose for thermal damage.

The specific mechanism of cell killing by hyperthermia is unknown, but the high activation energy of cell killing and other responses to hyperthermia suggest that protein denaturation is the rate-limiting step. Protein denaturation can be directly monitored by differential scanning calorimetry and in general there is a good correlation between protein denaturation and cellular response. Approximately 5% denaturation is necessary for detectable killing. Protein denaturation leads to the aggregation of both denatured and native protein with multiple effects on cellular function.

Adaptation, Physiological↗

PubMedDate not supplied

Simultaneous two-photon excitation of photofrin in relation to photodynamic therapy.

Photodynamic therapy (PDT), the use of light-activated drugs (photosensitizers), is an emerging treatment modality for tumors as well as various nononcologic conditions. Single-photon (1-gamma) PDT is limited by low specificity of the photosensitizer, leading to damage to healthy tissue adjacent to the diseased target tissue. One solution is to use simultaneous two-photon (2-gamma) excitation with ultrafast pulses of near-IR light. Due to the nonlinear interaction mechanism, 2-gamma excitation with a focused beam is localized in three dimensions, allowing treatment volumes on the order of femtoliters. We propose that this will be valuable in PDT of age-related macular degeneration (AMD), which causes blindness due to abnormal choroidal neovasculature and which is currently treated by 1-gamma PDT. Here, Photofrin has been used as the photosensitizer to demonstrate proof-of-principle of 2-gamma killing of vascular endothelial cells in vitro. The 2-gamma absorption properties of Photofrin were investigated in the 750-900 nm excitation wavelength range. It was shown that 2-gamma excitation dominates over 1-gamma excitation above 800 nm. The 2-gamma absorption spectrum of Photofrin in the 800-900 nm excitation wavelength range was measured. The 2-gamma cross section decreased from about 10 GM (1 GM = 10(-50) cm4 s/photon) at 800 nm to 5 GM at 900 nm. Adherent YPEN-1 endothelial cells were then incubated with Photofrin for 24 h and then treated by PDT at 850 nm where the 1-gamma contribution was negligible. Cell death was monitored with the use of 2-gamma scanning laser microscopy. The light doses required for killing were high (6300 J cm(-2) for approximately 50% killing), but 2-gamma cytotoxicity was unequivocally demonstrated. Although Photofrin is, per se, not a good choice for 2-gamma PDT due to its low 2-gamma cross section, this work provides baseline data to guide the development of novel photosensitizers with much higher 2-gamma cross sections (>100 GM), which will be required for 2-gamma PDT of AMD (and other conditions) to be clinically practical.

Aging↗