A fractal analysis of protein to DNA binding kinetics using biosensors

A fractal analysis of a confirmative nature only is presented for the binding of estrogen receptor (ER) in solution to its corresponding DNA (estrogen response element, ERE) immobilized on a sensor chip surface [J. Biol. Chem. 272 (1997) 11384], and for the cooperative binding of human 1,25-dihydroxyvitamin D(3) receptor (VDR) to DNA with the 9-cis-retinoic acid receptor (RXR) [Biochemistry 35 (1996) 3309]. Ligands were also used to modulate the first reaction. Data taken from the literature may be modeled by using a single- or a dual-fractal analysis. Relationships are presented for the binding rate coefficient as a function of either the analyte concentration in solution or the fractal dimension that exists on the biosensor surface. The binding rate expressions developed exhibit a wide range of dependence on the degree of heterogeneity that exists on the surface, ranging from sensitive (order of dependence equal to 1.202) to very sensitive (order of dependence equal to 12.239). In general, the binding rate coefficient increases as the degree of heterogeneity or the fractal dimension of the surface increases. The predictive relationships presented provide further physical insights into the reactions occurring on the biosensor surface. Even though these reactions are occurring on the biosensor surface, the relationships presented should assist in understanding and in possibly manipulating the reactions occurring on cellular surfaces.     

Analyte-receptor binding on surface plasmon resonance biosensors: a fractal analysis of Cre-loxP interactions and the influence of Cl, O, and S on drug-liposome interactions

A fractal analysis of the association and dissociation (whereever applicable) of Cre-loxP interactions and drug-liposome interactions on a sensor chip surface is presented. In both of these cases a dual-fractal analysis is required to adequately describe the association kinetics. The dissociation kinetics for Cre-loxP interactions is adequately described by a single-fractal analysis. The dual-fractal analysis used to describe the association kinetics of Cre-loxP interactions is consistent with the original two-step mechanism presented using a surface plasmon resonance biosensor. Our analysis includes both diffusion and surface effects by introducing the fractal dimension which makes quantitative the degree of heterogeneity on the sensor chip surface. Affinities are provided. Only the association kinetics were analysed for drug-liposome interactions since the initial sections of the dissociation curves were too steep to obtain reasonable drug-liposome complex concentration values on the sensor chip with time. Attempts made to relate the association rate coefficients with the molecular weight of the drug were unsuccessful. On using desipramine and imipramine as "arbitrarily selected standards" or "references" (only C, H, and N atoms present), it was noticed from the data analysed that the inclusion of the O and S atoms in the drug leads to a decrease in the association rate coefficients, ka1 (or k1) and ka2 (or k2) (compared with the arbitrarily selected standards or references). Similarly, the addition of the Cl atom in the drug leads to an increase in the association rate coefficient (compared with the arbitrarily selected standards or references). More data needs to be analysed to determine whether this is true for other drugs also.     

A mathematical analysis using fractals for binding interactions of nuclear estrogen receptors occurring on biosensor surfaces

A mathematical approach using fractal concepts is presented for modeling the binding and dissociation interactions between analytes and nuclear estrogen receptors (ER) occurring on surface plasmon resonance biosensor chip surfaces. A kinetic knowledge of the binding interactions mediated by ER would help in better understanding the carcinogenicity of these steroidogenic compounds and assist in modulating these reactions. The fractal approach is applied to analyte-ER interaction data obtained from literature. Numerical values obtained for the binding and dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D(f)) present on the biosensor surface. For example, a single-fractal analysis is used to describe the binding and dissociation phases for the binding of estradiol and ERalpha in solution to clone 31 protein immobilized on a biosensor chip (C-S. Suen et al., 1998, J. Biol. Chem. 273(42), 27645-27653). The binding and the dissociation rate coefficients are 27.57 and 8.813, respectively, and the corresponding fractal dimensions are 1.986 and 2.268, respectively. In some examples dual-fractal models were employed to obtain a better fit of either the association or the dissociation phases or for both. Predictive relationships are developed for (a) the binding and the dissociation rate coefficients as a function of their respective fractal dimensions and (b) the ratio K(A) (= k/k(d)) as a function of the ratio of the fractal dimensions (D(f)/D(fd)). The analysis should provide further physical insights into the ER-mediated interactions occurring on biosensor and other surfaces.     

A kinetic study of analyte-receptor binding and dissociation, and dissociation alone, for biosensor applications: a fractal analysis

A fractal analysis is presented for (a) analyte-receptor binding and dissociation kinetics and (b) dissociation kinetics alone for biosensor applications. Emphasis is placed on dissociation kinetics. Data taken from the literature may be modeled, in the case of binding, using a single-fractal analysis or a dual-fractal analysis. The dual-fractal analysis represents a change in the binding mechanism as the reaction progresses on the surface. A single-fractal analysis is adequate to model the dissociation kinetics in the examples presented. Predictive relationships developed for the dissociation rate coefficient(s) as a function of the analyte concentration are of particular value since they provide a means by which the dissociation rate coefficients may be manipulated. Relationships are also presented for the binding and dissociation rate coefficients as a function of their corresponding fractal dimension, D(f), or the degree of heterogeneity that exists on the surface. When analyte-receptor binding or dissociation is involved, an increase in the heterogeneity on the surface (increase in D(f)) leads to an increase in the binding and in the dissociation rate coefficient.     

A kinetic study of analyte-receptor binding and dissociation for biosensor applications: a fractal analysis for two different DNA systems

A fractal analysis of DNA binding and dissociation kinetics on biosensor surfaces is presented. The fractal approach provides an attractive, convenient method to model the kinetic data taking into account the effects of surface heterogeneity brought about by ligand immobilization. The fractal technique can be used in conjunction or as an alternate approach to conventional modeling techniques, such as the Langmuir model, saturation model, etc. Examples analyzed include a DNA molecular beacon biosensor and a plasmid DNA-(cationic polymer) interaction biosensor. The molecular beacon example provides some insights into the nature of the surface and how it influences the binding rate coefficients. The DNA-cationic polymer interaction example provides some quantitative results on the binding and dissociation rate coefficients. Data taken from the literature may be modeled, in the case of binding, using a single-fractal analysis or a dual-fractal analysis. The dual-fractal analysis results indicate a change in the binding mechanism as the reaction progresses on the surface. A single-fractal analysis is adequate to model the dissociation kinetics in the example presented. Relationships are presented for the binding rate coefficients as a function of their corresponding fractal dimension, D(f), which is an indication of the degree of heterogeneity that exists on the surface. When analyte-receptor binding is involved, an increase in the heterogeneity of the surface (increase in D(f)) leads to an increase in the binding rate coefficient.     

Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis

Abstract

Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simulations permit researchers to obtain structural information about these proteins, and principal component analysis (PCA) allows for the identification of collective motions. There are available structures for the active form (3QAK) and the inactive form (3EML) of A2AR which permit us to gain insight about their activation/inactivation mechanism. In this work, we have proposed an inverse strategy using MD simulations where the active form was coupled to the antagonist caffeine and the inactive form was coupled to adenosine agonist. Moreover, we have included four reported thermostabilizing mutations in the inactive form to study A2AR structural differences under different conditions. Some observations stand out from the PCA studies. For instance, the apo structures showed remarkable similarities, and the principal components (PCs) were rearranged in a ligand-dependent manner. Additionally, the active conformation was less stable compared to the inactive one. Some PCs inverted their direction in the presence of a ligand, and comparison of the PCs between 3EML and 3EML_ADN showed that adenosine induced major changes in the structure of A2AR. Rearrangement of PCs precedes and drives conformational changes that occur after ligand binding. Knowledge about these conformational changes provides important insights about the activity of A2AR.     

Binding and dissociation kinetics using fractals: an analysis of electrostatic effects and randomly coupled and oriented coupled receptors on biosensor surfaces

A fractal analysis is used to analyze the influence of: (a) electrostatic interactions on binding and dissociation rate coefficients for antibodies HH8, HH10, and HH26 in solution to hen egg-white lysozyme (HEL) immobilized on a sensor chip surface [Biophys. J. 83 (2002) 2946]; and (b) the binding and dissociation of recombinant Fab in solution to random NHS-coupled Cys-HEL and oriented thiol-coupled Cys-HEL immobilized on a sensor chip surface [Methods 20 (2000) 310]. Single- and dual-fractal models were employed to fit the data. Values of the binding and the dissociation rate coefficient(s) and the fractal dimensions were obtained from a regression analysis provided by Corel Quattro Pro 8.0 (Corel Corporation Limited, Ottawa, Canada. 1997). The binding rate coefficients are quite sensitive to the degree of heterogeneity on the sensor chip surface. It is of interest to compare the results obtained by the fractal analysis with that of the original analysis [Biophys. J. 83 (2002) 2946]. For example, as one goes from the binding of 21 nM HH10/HEL to the binding of 640 nM HH10/HEL(K97A), Sinha et al. [Biophys. J. 83 (2002) 29461 indicate that the enhancement of diffusional encounter rates may be due to 'electrostatic steering' (a long-range interaction). Our analysis indicates that there is an increase in the value of the fractal dimension, Df1 by a factor of 1.12 from a value of 2.133-2.385. This increase in the degree of heterogeneity on the surface leads to an increase in the binding rate coefficient, k1 by a factor of 1.59 from 12.92 to 20.57. The fractal analysis of binding and dissociation of recombinant Fab in solution to random NHS-coupled Cys-HEL and oriented thiol-coupled Cys-HEL immobilized on a sensor chip [Methods 20 (2000) 310] surface are consistent with the degree of heterogeneity present on the sensor chip surface for the random and the oriented case. As expected, the random case will exhibit a higher degree of heterogeneity than the oriented case, leading to subsequently a higher binding rate coefficient.     

Analysis of neuropeptide Y-induced feeding: dissociation of Y1 and Y2 receptor effects on natural meal patterns.

To differentiate NPY receptor subtypes, Y₁ and Y₂, in terms of their impact on feeding behavior, the intact molecule NPY(1–36) and the 3 fragments, NPY(2–36), the Y₁ agonist [Leu³¹,Pro³⁴]NPY, and the Y₂ agonist NPY(13–36), were injected (100 pmol/0.3 μl) into the hypothalamic paraventricular nucleus (PVN) of freely feeding rats. A computer-automated data acquisition system was employed in these experiments to permit a detailed analysis of feeding over the 12-h nocturnal cycle, in animals maintained on pure macronutrient diets. The results demonstrate that: 1) NPY(1–36) potentiates feeding behavior, primarily carbohydrate ingestion, by increasing the size and duration of the first meal after injection, rather than by affecting meal number or feeding rate, suggesting that NPY acts through mechanisms of satiety. The potentiation of carbohydrate intake occurs in association with a suppression of protein intake, which is strongest during the second meal after injection and which further increases the proportion of carbohydrate in the diet. No changes in fat ingestion are seen. 2) NPY(2–36), with the N-terminal tyrosine residue deleted, is equally potent to NPY(1–36) in potentiating carbohydrate intake and increasing meal size; however, it is less selective than NPY(1–36), producing an additional, smaller increase in consumption of protein. 3) The stimulatory effect of these peptides on carbohydrate intake and meal size is similarly observed, with somewhat reduced potency, after PVN injection of the selective Y₁ agonist [Leu³¹,Pro³⁴]NPY which, like NPY(1–36), also reduces protein intake. 4) The Y₂ receptor agonist, NPY(13–36), causes a decrease in the ingestion of carbohydrate, a smaller decline in protein intake, and a reduction in meal size. It is proposed that hypothalamic Y₁ receptors mediate the stimulatory effect of NPY on carbohydrate intake and meal size, while Y₂ receptors have the opposite effect of suppressing carbohydrate intake, possibly by altering presynaptic release of monoamines known to influence nutrient ingestion.     

Cardioprotective effects of adenosine A1 and A 3 receptor activation during hypoxia in isolated rat cardiac myocytes

Adenosine (ADO) is a well-known regulator of a variety of physiological functions in the heart. In stress conditions, like hypoxia or ischemia, the concentration of adenosine in the extracellular fluid rises dramatically, mainly through the breakdown of ATP. The degradation of adenosine in the ischemic myocytes induced damage in these cells, but it may simultaneously exert protective effects in the heart by activation of the adenosine receptors. The contribution of ADO to stimulation of protective effects was reported in human and animal hearts, but not in rat hearts. The aim of this study was to evaluate the role of adenosine A₁ and A₃ receptors (A₁R and A₃R), in protection of isolated cardiac myocytes of newborn rats from ischemic injury. The hypoxic conditions were simulated by exposure of cultured rat cardiomyocytes (4–5 days in vitro), to an atmosphere of a N₂ (95%) and CO₂ (5%) mixture, in glucose-free medium for 90 min. The cardiotoxic and cardioprotective effects of ADO ligands were measured by the release of lactate dehydrogenase (LDH) into the medium. Morphological investigation includes immunohistochemistry, image analysis of living and fixed cells and electron microscopy were executed. Pretreatment with the adenosine deaminase considerably increased the hypoxic damage in the cardiomyocytes indicating the importance of extracellular adenosine. Blocking adenosine receptors with selective A₁ and A₃ receptor antagonists abolished the protective effects of adenosine. A₁R and A₃R activation during the hypoxic insult delays onset of irreversible cell injury and collapse of mitochondrial membrane potential as assessed using DASPMI fluorochrom. Cardioprotection induced by the A₁R agonist, CCPA, was abolished by an A₁R antagonist, DPCPX, and was not affected by an A₃R antagonist, MRS1523. Cardioprotection caused by the A₃R agonist, Cl-IB-MECA, was antagonized completely by MRS1523 and only partially by DPCPX. Activation of both A₁R and A₃R together was more efficient in protection against hypoxia than by each one alone. Our study indicates that activation of either A₁ or A₃ adenosine receptors in the rat can attenuate myocyte injury during hypoxia. Highly selective A₁R and A₃R agonists may have potential as cardioprotective agents against ischemia or heart surgery.     

Mesolimbic and striatal dopamine receptor supersensitivity: prophylactic and reversal effects of L-prolyl-L-leucyl-glycinamide (PLG)

Functional supersensitivity of mesolimbic and striatal dopamine receptors has been suggested to contribute to the pathogenesis of schizophrenia and tardive dyskinesia. Using the rodent model of chronic administration of the neuroleptic haloperidol, we investigated the possible desensitizing effects of a tripeptide structurally unrelated to dopamine agonists, L-prolyl-L-leucyl-glycinamide (PLG) on mesolimbic and striatal dopaminergic receptor supersensitivity. Administration of PLG either prior to or after chronic haloperidol, inhibited the supersensitivity of dopamine receptors. The results have implications for pharmacological intervention in preventing tardive dyskinesia and relapse psychosis of schizophrenia.     

Biosorption of reactive and basic dyes using fermentation waste <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>: the effects of pH and salt concentration and characterization of the binding sites

A low cost biosorbent, Corynebacterium glutamicum, was studied for the sorption of Reactive Red 4 (RR 4) and Methylene Blue (MB). The equilibrium isotherm data were well described by the Langmuir model. pH edge experiments showed that pH of the solution was an important controlling parameter in the sorption process. In the case of RR 4, with increases in the pH from 2 to 10, the uptake decreased from 52 to 1 mg/g; conversely, the uptake of MB increased and the maximum MB uptake was obtained at pH ≥ 9. An increase in the salt concentration strongly influenced the uptake of MB, but had no effect on that of RR 4. In order to identify the binding sites for the dye molecules, the biosorbent was potentiometrically titrated, the results of which showed the presents of four major functional group types on the biomass surface, which were confirmed by FTIR analysis. It was found that positively charged amine groups (Biomass-NH₃ ⁺) were the likely binding sites for anionic RR 4, and negatively charged carboxyl (Biomass-COO⁻) and phosphate groups (Biomass-HPO₄ ⁻) played a role in the electrostatic attraction of cationic MB.     

Diabetes mellitus caused by mutations in human insulin: analysis of impaired receptor binding of insulins Wakayama,Los Angeles and Chicago using pharmacoinformatics

Several naturally occuring mutations in the human insulin gene are associated with diabetes mellitus. The three known mutant molecules, Wakayama, Los Angeles and Chicago were evaluated using molecular docking and molecular dynamics (MD) to analyse mechanisms of deprived binding affinity for insulin receptor (IR). Insulin Wakayama, is a variant in which valine at position A3 is substituted by leucine, while in insulin Los Angeles and Chicago, phenylalanine at positions B24 and B25 is replaced by serine and leucine, respectively. These mutations show radical changes in binding affinity for IR. The ZDOCK server was used for molecular docking, while AMBER 14 was used for the MD study. The published crystal structure of IR bound to natural insulin was also used for MD. The binding interactions and MD trajectories clearly explained the critical factors for deprived binding to the IR. The surface area around position A3 was increased when valine was substituted by leucine, while at positions B24 and B25 aromatic amino acid phenylalanine replaced by non-aromatic serine and leucine might be responsible for fewer binding interactions at the binding site of IR that leads to instability of the complex. In the MD simulation, the normal mode analysis, rmsd trajectories and prediction of fluctuation indicated instability of complexes with mutant insulin in order of insulin native insulin < insulin Chicago < insulin Los Angeles < insulin Wakayama molecules which corresponds to the biological evidence of the differing affinities of the mutant insulins for the IR.     

Mechanism of C2-toxin inhibition by fluphenazine and related compounds: investigation of their binding kinetics to the C2II-channel using the current noise analysis

The binding component C2II of the binary actin ADP-ribosylating C2-toxin from Clostridium botulinum is essential for intoxication of target cells. Activation by a protease leads to channel formation and this is presumably required for the transport of the toxic C2I component into cells. The C2II-channel is cation selective and contains a binding site for fluphenazine and structurally related compounds. Ion transport through C2II and in vivo intoxication is blocked when the sites are occupied by the ligands. C2II was reconstituted into artificial lipid bilayer membranes and formed ion permeable channels. The binding constant of chloroquine, primaquine, quinacrine, chloropromazine and fluphenazine to the C2II-channel was determined using titration experiments, which resulted in its block. The ligand-induced current noise of the C2II-channels was investigated using fast Fourier transformation. The noise of the open channels had a rather small spectral density, which was a function of the inverse frequency up to about 100 Hz. Upon addition of ligands to the aqueous phase the current through C2II decreased in a dose-dependent manner. Simultaneously, the spectral density of the current noise increased drastically and its frequency dependence was of Lorentzian type, which was caused by the on and off-reactions of the ligand-mediated channel block. The ligand-induced current noise of C2II was used for the evaluation of the binding kinetics for different ligands to the channel. The on-rate constant of ligand binding was between 10(7) and 10(9) M(-1) s(-1) and was dependent on the ionic strength of the aqueous phase. The off-rate varied between about 10 s(-1) and 3900 s(-1) and depended on the structure of the ligand. The role of structural requirements for the effective block of C2II by the different ligands is discussed.     

Dual character of Toll-like receptor signaling: Pro-tumorigenic effects and anti-tumor functions

As a major class of pattern-recognition receptors, Toll-like receptors (TLRs) play a critical role in defense against invading pathogens. Increasing evidence demonstrates that, in addition to infection, TLRs are involved in other important pathological processes, such as tumorigenesis. Activation of TLRs results in opposing outcomes, pro-tumorigenic effects and anti-tumor functions. TLR signaling can inhibit apoptosis and promote chronic inflammation-induced tumorigenesis. TLR activation in tumor cells and immune cells can induce production of cytokines, increase tumor cell proliferation and apoptosis resistance, promote invasion and metastasis, and inhibit immune cell activity resulting in tumor immune escape. In contrast, the engagement of other TLRs directly induces growth inhibition and apoptosis of tumor cells and triggers activation of immune cells enhancing anti-tumor immune responses. Thus, the interpretation of the precise function of each TLR in tumors is very important for targeting TLRs and using TLR agonists in tumor therapy. We review the role of TLR signaling in tumors and discuss the factors that affect outcomes of TLR activation.     

Discovery of naldemedine: A potent and orally available opioid receptor antagonist for treatment of opioid-induced adverse effects

Structure-activity relationship studies of several morphinan derivatives were conducted to obtain dual antagonists for μ- and δ-opioid receptors. We discovered peripherally restricted dual antagonists for μ/δ-opioid receptors as a new chemotype with a morphinan scaffold, which are orally available and do not easily pass the blood–brain barrier. As we expected, some of these compounds inhibit opioid-induced constipation and emesis/vomiting with limited potential to interfere the analgesic effects of morphine. Among them, naldemedine was selected as a potential drug candidate.     

A novel series of 4-methyl substituted pyrazole derivatives as potent glucagon receptor antagonists: Design,synthesis and evaluation of biological activities

A novel series of 4-methyl substituted pyrazole derivatives were designed, synthesized and biologically evaluated as potent glucagon receptor (GCGR) antagonists. In this study, compounds 9q, 9r, 19d and 19e showed high GCGR binding (IC₅₀?=?0.09?μM, 0.06?μM, 0.07?μM and 0.08?μM, respectively) and cyclic-adenosine monophosphate (cAMP) activities (IC₅₀?=?0.22?μM, 0.26?μM, 0.44?μM and 0.46?μM, respectively) in cell-based assays. Most importantly, the docking experiment demonstrated that compound 9r formed extensive hydrophobic interactions with the receptor binding pocket, making it justifiable to further investigate the potential of becoming a GCGR antagonist.     

Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis

Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease with physical barriers and neurological disorders. The objective of this study was to explore the differentially expressed genes (DEGs) in OPLL patient ligament cells and identify the target sites for the prevention and treatment of OPLL in clinic. Gene expression data GSE5464 was downloaded from Gene Expression Omnibus; then DEGs were screened by limma package in R language, and changed functions and pathways of OPLL cells compared to normal cells were identified by DAVID (The Database for Annotation, Visualization and Integrated Discovery); finally, an interaction network of DEGs was constructed by string. A total of 1536 DEGs were screened, with 31 down-regulated and 1505 up-regulated genes. Response to wounding function and Toll-like receptor signaling pathway may involve in the development of OPLL. Genes, such as PDGFB, PRDX2 may involve in OPLL through response to wounding function. Toll-like receptor signaling pathway enriched genes such as TLR1, TLR5, and TLR7 may involve in spine cord injury in OPLL. PIK3R1 was the hub gene in the network of DEGs with the highest degree; INSR was one of the most closely related genes of it. OPLL related genes screened by microarray gene expression profiling and bioinformatics analysis may be helpful for elucidating the mechanism of OPLL.     

Molecular dynamics simulation of the effects of single (S221P) and double (S221P and K216E) mutations in the hemagglutinin protein of influenza A H5N1 virus: a study on host receptor specificity

Avian influenza viruses of subtype H5N1 circulating in animals continue to pose threats to human health. The binding preference of the viral surface protein hemagglutinin (HA) to sialosaccharides of receptors is an important area for understanding mutations in the receptor binding site that could be the cause for avian-to-human transmission. In the present work, we studied the effect of two receptor binding site mutations, S221P singly and in combination with another mutation K216E in the HA protein of influenza A H5N1 viruses. Docking of sialic acid ligands corresponding to both avian and human receptors and molecular dynamics simulations of the complexes for wild and mutant strains of H5N1 viruses were carried out. The H5N1 strain possessing the S221P mutation indicated decreased binding to α2,3-linked sialic acids (avian receptor, SAα2,3Gal) when compared to the binding of the wild-type strain that did not possess the HA-221 mutation. The binding to α2,6-linked sialic acids (human receptor, SAα2,6Gal) was found to be comparable, indicating that the mutant strain shows limited dual receptor specificity. On the other hand, the S221P mutation in synergism with the K216E mutation in the binding site, resulted in increased binding affinity for SAα2,6Gal when compared to SAα2,3Gal, indicative of enhanced binding to human receptors. The in-depth study of the molecular interactions in the docked complexes could explain how co-occurring mutations in the HA viral protein can aid in providing fitness advantage to the virus, in the context of host receptor specificity in emerging variants of H5N1 influenza viruses.     

Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure

The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the transition state for folding as well as in the denatured state. The perturbed native state pK(a) of D8 (pK(a) = 3.0) appears to be maintained through non-native interactions in both the transition state and the denatured state. Mutational effects on the stability of the transition state for protein (un)folding are often analyzed in respect to change in ground states. Thus, the interpretation of transition state analysis critically depends on an understanding of mutational effects on both the native and denatured state. Increasing evidence for structurally biased denatured states under physiological conditions raises concerns about possible denatured state effects on folding studies. We show that the structural interpretation of transition state analysis can be altered dramatically by denatured state effects.