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1.
Bioorg Med Chem Lett ; 92: 129392, 2023 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-37364726

RESUMEN

The depletion of the neurotransmitter acetylcholine has been suggested to contribute to the reduced cognitive function observed in individuals suffering from neurodegenerative diseases such as Alzheimer's Disease (AD). For the two major cholinesterases, butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), increased BChE activity observed in individuals with AD has been suggested to deplete acetylcholine levels. To reduce acetylcholine degradation and help restore the pool of the neurotransmitter, specific and potent BChE inhibitors are sought. Our previous findings have identified 9-fluorenylmethoxycarbonyl (Fmoc) amino acid-based inhibitors as effective BChE inhibitors. The amino acid-based compounds offered the opportunity to survey a range of structural features to enhance interactions with the enzyme active site. As enzymes interact with features of their substrates, incorporation of substrate-like features was predicted to lead to better inhibitors. Specifically, incorporation of a trimethylammonium moiety to mimic the cationic group of acetylcholine may lead to increased potency and selectivity. To test this model, a series of inhibitors bearing a cationic trimethylammonium group were synthesized, purified, and characterized. While the Fmoc-ester derivatives inhibited the enzyme, additional experiments showed the compounds acted as substrates and were enzymatically hydrolyzed. Inhibition studies with the Fmoc-amide derivatives showed that the compounds do not act as substrates and selectively inhibit BChE with IC50 values in the 0.06-10.0 µM range. Computational docking studies suggest that the inhibitors can interact with cholinyl binding site and peripheral site. Overall, the results suggest that introducing substrate-like characteristics within the Fmoc-amino acid-based background increases their potency. The versatile and ready access to amino acid-based compounds offers an attractive system to further our understanding of the relative importance of protein-small molecule interactions while guiding the development of better inhibitors.


Asunto(s)
Enfermedad de Alzheimer , Butirilcolinesterasa , Humanos , Acetilcolina , Acetilcolinesterasa/metabolismo , Enfermedad de Alzheimer/metabolismo , Aminoácidos/farmacología , Butirilcolinesterasa/metabolismo , Inhibidores de la Colinesterasa/química , Simulación del Acoplamiento Molecular , Relación Estructura-Actividad , Compuestos de Amonio Cuaternario/química
2.
Biopolymers ; 113(11): e23525, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-36106525

RESUMEN

Over the past 3.5 billion years of evolution, enzymes have adopted a myriad of conformations to suit life on earth. However, torsional angles of proteins have settled into limited zones of energetically favorable dihedrals observed in Ramachandran plots. Areas outside said zones are believed to be disallowed to all amino acids, except glycine, due to steric hindrance. Triosephosphate isomerase (TIM), a homodimer with a catalytic rate approaching the diffusion limit, contains an active site lysine residue (K13) with dihedrals within the fourth quadrant (Φ = +51/Ψ = -143). Both the amino acid and the dihedral angles are conserved across all species of TIM and known crystal structures regardless of ligand. Only crystal structures of the engineered monomeric version (1MSS) show accepted ß-sheet dihedral values of Φ = -135/Ψ = +170 but experiments show a 1000-fold loss in activity. Based on these results, we hypothesized that adopting the unfavorable torsion angle for K13 contributes to catalysis. Using both, computational and experimental approaches, four residues that interact with K13 (N11, M14, E97, and Q64) were mutated to alanine. In silico molecular dynamics (MD) simulations were performed using 2JK2 unliganded human TIM as a starting structure. Ramachandran plots, containing K13 dihedral values reveal full or partial loss of disallowed zone angles. N11A showed no detectable catalytic activity and lost the unfavorable K13 dihedral angles across four separate force fields during simulation while all other mutants plus wild type retained activity and retained the conserved K13 dihedral angles.


Asunto(s)
Proteínas , Triosa-Fosfato Isomerasa , Humanos , Triosa-Fosfato Isomerasa/genética , Triosa-Fosfato Isomerasa/química , Conformación Proteica , Proteínas/química , Ligandos , Aminoácidos
3.
Anal Biochem ; 654: 114796, 2022 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-35772490

RESUMEN

The use of cosolvents to solubilize compounds under investigation while having minimal effects on enzyme activity is an important component in many biochemical studies. Predicting the effects of cosolvents on enzyme activity can be complicated, as enzymes with similar overall structures might exhibit different behaviors in different cosolvents. In this study, the effects of several commonly used cosolvents: Methanol, acetonitrile, acetone, and dimethyl sulfoxide (DMSO), on two cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), were evaluated. Although the overall structures are highly similar, AChE activity was more sensitive to the organic cosolvents tested compared to BChE. Effects of the cosolvents on activity did not vary over time and activity was restored upon dilution of the cosolvent. Michaelis-Menten kinetics experiments showed that Vmax values were not substantially affected, while KM values increased up to ∼20-fold for AChE and ∼4-fold for BChE in the presence of 5% DMSO or acetone. The results suggest that BChE demonstrates more robustness to its cosolvent environment compared to AChE, and that cosolvents effects may arise from the molecules acting as inhibitors. The results may aid decisions of cosolvents used in enzyme assays and may help guide experimental conditions and design when conducting experiments comparing different enzymes.


Asunto(s)
Acetilcolinesterasa , Butirilcolinesterasa , Acetona , Acetilcolinesterasa/química , Butirilcolinesterasa/química , Inhibidores de la Colinesterasa/química , Inhibidores de la Colinesterasa/farmacología , Dimetilsulfóxido/farmacología
4.
Bioorg Med Chem Lett ; 30(13): 127213, 2020 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-32381396

RESUMEN

A small library of new organophosphorylated warfarins and 3-benzylcoumarins were synthesized and evaluated for in vitro cholinesterase inhibition by Ellman's method. Most of the compounds were found to be selective for butyrylcholinesterase (BChE) over acetylcholinesterase (AChE), with IC50 values ranging from 0.363 µM to 53.0 µM determined after 15 s of enzyme exposure. Comparison of the most potent compound, 3b with its constitutional isomer 2b revealed the high importance of phosphate positioning. Reversed selectivity and a 100-fold reduction in anti-BChE activity was observed when the organophosphate was attached to the benzyl instead of the coumarin. Docking calculations suggest that 3b binds initially as a transition state mimic with near-optimal phosphate orientation relative to S198 and occupation of the oxyanion hole prior to phosphorylation. These results might inspire the design of a new type of non-neuropathic and irreversible coumarin-based inhibitor against BChE.


Asunto(s)
Butirilcolinesterasa/metabolismo , Inhibidores de la Colinesterasa/farmacología , Organofosfatos/farmacología , Warfarina/análogos & derivados , Warfarina/farmacología , Animales , Inhibidores de la Colinesterasa/síntesis química , Inhibidores de la Colinesterasa/metabolismo , Electrophorus , Caballos , Humanos , Simulación del Acoplamiento Molecular , Estructura Molecular , Organofosfatos/síntesis química , Organofosfatos/metabolismo , Unión Proteica , Relación Estructura-Actividad , Warfarina/metabolismo
5.
J Biomol Struct Dyn ; 38(4): 1028-1041, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-30909811

RESUMEN

All-atom molecular dynamics simulations of butyrylcholinesterase (BChE) sans inhibitor and in complex with each of 15 dialkyl phenyl phosphate derivatives were conducted to characterize inhibitor binding modes and strengths. Each system was sampled on the 250 ns timescale in explicit ionic solvent, for a total of over 4 µs of simulation time. A K-means algorithm was used to cluster the resulting structures into distinct binding modes, which were further characterized based on atomic-level contacts between inhibitor chemical groups and active site residues. Comparison of experimentally observed inhibition constants (KI) with the resulting contact tables provides structural explanations for relative binding coefficients and highlights several notable interaction motifs. These include ubiquitous contact between glycines in the oxyanion hole and the inhibitor phosphate group; a sterically driven binding preference for positional isomers that extend aromaticity; a stereochemical binding preference for choline-containing inhibitors, which mimic natural BChE substrates; and the mechanically induced opening of the omega loop region to fully expose the active site gorge in the presence of choline-containing inhibitors. Taken together, these observations can greatly inform future design of BChE inhibitors, and the approach reported herein is generalizable to other enzyme-inhibitor systems and similar complexes that depend on non-covalent molecular recognition.Communicated by Ramaswamy H. Sarma.


Asunto(s)
Butirilcolinesterasa/química , Inhibidores de la Colinesterasa/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Sitios de Unión , Dominio Catalítico , Inhibidores de la Colinesterasa/farmacología , Humanos , Ligandos , Conformación Molecular , Estructura Molecular , Unión Proteica , Relación Estructura-Actividad
6.
Biochem Biophys Res Commun ; 505(2): 492-497, 2018 10 28.
Artículo en Inglés | MEDLINE | ID: mdl-30268499

RESUMEN

Investigating enzyme activity is central to our understanding of biological function, and the design of biocatalysts continues to find applications in synthesis. While a role for active site residues can be proposed based on structure and mechanism, our understanding of the catalytic importance for residues surrounding the active site is less well understood. In triosephosphate isomerase (TIM), Glu97 is situated adjacent to the active site and is found in essentially all sequences. Prior studies reported mutation of Glu97 to Asp and Gln in TIM from Plasmodium falciparum (PfTIM) led to a 100- and 4000-fold decrease in activity, respectively, while the E97D mutation in TIM from Gallus gallus (cTIM) had no effect on activity. To investigate further the question of how mutations in essentially superimposable structures give different effects, we mutated E97 in TIM from Trypanosoma brucei brucei (TbbTIM), Saccharomyces cerevisiae (yTIM), and human (hTIM). The E97D, E97A, and E97Q mutations led to a ∼three-tenfold decrease in activity, a modest effect compared to the 102-103-fold effect in PfTIM. CD and fluorescence studies showed the overall structures for the mutants were essentially unchanged. Structural analysis shows that several residues surrounding E97 differ between PfTIM and TIM from the other organisms, and rearrangements or mispositioning of residues in PfTIM may lead to the different rate effects. The results illustrate the interplay of active site and surrounding residues in affecting catalysis and highlight that understanding of the role of residues surrounding the active site may aid in the incorporation of favorable or avoidance of unfavorable interactions when designing enzymes.


Asunto(s)
Ácido Glutámico/química , Triosa-Fosfato Isomerasa/química , Biocatálisis , Dominio Catalítico , Humanos , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Triosa-Fosfato Isomerasa/genética , Triosa-Fosfato Isomerasa/metabolismo , Trypanosoma brucei brucei/enzimología
7.
J Am Chem Soc ; 140(31): 9827-9843, 2018 08 08.
Artículo en Inglés | MEDLINE | ID: mdl-29990421

RESUMEN

Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, with smaller perturbations for more remote hydrogen bonds. Across 19 measurements in three systems, the length change in one oxyanion hole hydrogen bond was propagated to the other, by a factor of -0.30 ± 0.03. This common effect suggests that hydrogen bond coupling is minimally influenced by the remaining protein scaffold. The observed coupling is reproduced by molecular mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations for changes to a proximal oxyanion hole hydrogen bond. However, effects from distal hydrogen bonds are reproduced only by QM/MM, suggesting the importance of polarization in hydrogen bond coupling. These results deepen our understanding of hydrogen bonds and their networks, providing strong evidence for long-range coupling and for the extent of this coupling. We provide a broadly predictive quantitative relationship that can be applied to and can be further tested in new systems.


Asunto(s)
Proteínas Bacterianas/química , Cetosteroides/química , Fotorreceptores Microbianos/química , Esteroide Isomerasas/química , Dominio Catalítico , Cristalografía por Rayos X , Enlace de Hidrógeno , Espectroscopía de Protones por Resonancia Magnética
9.
Bioorg Med Chem ; 25(12): 3171-3181, 2017 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-28416102

RESUMEN

A series of dialkyl aryl phosphates and dialkyl arylalkyl phosphates were synthesized. Their inhibitory activities were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The di-n-butyl phosphate series consistently displayed selective inhibition of BChE over AChE. The most potent inhibitors of butyrylcholinesterase were di-n-butyl-3,5-dimethylphenyl phosphate (4b) [KI=1.0±0.4µM] and di-n-butyl 2-naphthyl phosphate (5b) [KI=1.9±0.4µM]. Molecular modeling was used to uncover three subsites within the active site gorge that accommodate the three substituents attached to the phosphate group. Phosphates 4b and 5b were found to bind to these three subsites in analogous fashion with the aromatic groups in both analogs being accommodated by the "lower region," while the lone pairs on the PO oxygen atoms were oriented towards the oxyanion hole. In contrast, di-n-butyl-3,4-dimethylphenyl phosphate (4a) [KI=9±1µM], an isomer of 4b, was found to orient its aromatic group in the "upper left region" subsite as placement of this group in the "lower region" resulted in significant steric hindrance by a ridge-like region in this subsite. Future studies will be designed to exploit these features in an effort to develop inhibitors of higher inhibitory strength against butyrylcholinesterase.


Asunto(s)
Butirilcolinesterasa/metabolismo , Inhibidores de la Colinesterasa/química , Inhibidores de la Colinesterasa/farmacología , Naftalenos/química , Naftalenos/farmacología , Organofosfatos/química , Organofosfatos/farmacología , Compuestos Organofosforados/química , Compuestos Organofosforados/farmacología , Acetilcolinesterasa/efectos de los fármacos , Acetilcolinesterasa/metabolismo , Animales , Bovinos , Inhibidores de la Colinesterasa/síntesis química , Electrophorus , Caballos , Humanos , Simulación del Acoplamiento Molecular , Naftalenos/síntesis química , Organofosfatos/síntesis química , Compuestos Organofosforados/síntesis química , Relación Estructura-Actividad
10.
Bioorg Med Chem Lett ; 27(11): 2410-2414, 2017 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-28416133

RESUMEN

The sulfinic acid analog of aspartic acid, cysteine sulfinic acid, introduces a sulfur atom that perturbs the acidity and oxidation properties of aspartic acid. Cysteine sulfinic acids are often introduced in peptides and proteins by oxidation of cysteine, but this method is limited as all cysteine residues are oxidized and cysteine residues are often oxidized to sulfonic acids. To provide the foundation for the specific incorporation of cysteine sulfinic acids in peptides and proteins, we synthesized a 9-fluorenylmethyloxycarbonyl (Fmoc) benzothiazole sulfone analog. Oxidation conditions to generate the sulfone were examined and oxidation of the Fmoc-protected sulfide (3) with NbC in hydrogen peroxide provided the corresponding sulfone (4) in the highest yield and purity. Reduction with sodium borohydride generated the cysteine sulfinic acid (5) suggesting this approach may be an efficient method to incorporate a cysteine sulfinic acid in biomolecules. A model tripeptide bearing a cysteine sulfinic acid was synthesized using this approach. Future studies are aimed at using this method to incorporate cysteine sulfinic acids in peptide hormones and proteins for use in the study of biological function.


Asunto(s)
Cisteína/análogos & derivados , Cisteína/síntesis química , Péptidos/síntesis química , Ácidos Sulfínicos/síntesis química , Benzotiazoles/síntesis química , Oxidación-Reducción , Técnicas de Síntesis en Fase Sólida , Solubilidad , Estereoisomerismo
11.
Amino Acids ; 48(12): 2755-2763, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27522651

RESUMEN

Cholinesterases are involved in neuronal signal transduction, and perturbation of function has been implicated in diseases, such as Alzheimer's and Huntington's disease. For the two major classes of cholinesterases, such as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), previous studies reported BChE activity is elevated in patients with Alzheimer's disease, while AChE levels remain the same or decrease. Thus, the development of potent and specific inhibitors of BChE have received much attention as a potential therapeutic in the alleviation of neurodegenerative diseases. In this study, we evaluated amino acid analogs as selective inhibitors of BChE. Amino acid analogs bearing a 9-fluorenylmethyloxycarbonyl (Fmoc) group were tested, as the Fmoc group has structural resemblance to previously described inhibitors. We identified leucine, lysine, and tryptophan analogs bearing the Fmoc group as selective inhibitors of BChE. The Fmoc group contributed to inhibition, as analogs bearing a carboxybenzyl group showed ~tenfold higher values for the inhibition constant (K I value). Inclusion of a t-butoxycarbonyl on the side chain of Fmoc tryptophan led to an eightfold lower K I value compared to Fmoc tryptophan alone suggesting that modifications of the amino acid side chains may be designed to create inhibitors with higher affinity. Our results identify Fmoc-amino acids as a scaffold upon which to design BChE-specific inhibitors and provide the foundation for further experimental and computational studies to dissect the interactions that contribute to inhibitor binding.


Asunto(s)
Enfermedad de Alzheimer/enzimología , Aminoácidos/química , Butirilcolinesterasa/química , Inhibidores de la Colinesterasa/farmacología , Fluorenos/química , Acetilcolinesterasa/química , Enfermedad de Alzheimer/tratamiento farmacológico , Aminoácidos/farmacología , Butirilcolinesterasa/metabolismo , Inhibidores de la Colinesterasa/química , Fluorenos/farmacología , Humanos , Leucina/química , Lisina/química , Unión Proteica , Triptófano/química
13.
Science ; 349(6251): 936, 2015 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-26315426

RESUMEN

Fried et al. (Reports, 19 December 2014, p. 1510) demonstrated a strong correlation between reaction rate and the carbonyl stretching frequency of a product analog bound to ketosteroid isomerase oxyanion hole mutants and concluded that the active-site electric field provides 70% of catalysis. Alternative comparisons suggest a smaller contribution, relative to the corresponding solution reaction, and highlight the importance of atomic-level descriptions.


Asunto(s)
Cetosteroides/metabolismo , Electricidad Estática , Esteroide Isomerasas/química
14.
J Am Chem Soc ; 136(21): 7643-54, 2014 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-24787954

RESUMEN

Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via "short, strong" or "low-barrier" hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater "sensitivity") to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr's) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic environment that greatly enhances the energetic response to charge accumulation, consistent with prior experimental results.


Asunto(s)
Aminoácidos/química , Cetosteroides/química , Esteroide Isomerasas/metabolismo , Aniones , Dominio Catalítico , Enlace de Hidrógeno , Cetosteroides/metabolismo , Conformación Proteica , Esteroide Isomerasas/química
15.
Biochemistry ; 53(15): 2541-55, 2014 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-24597914

RESUMEN

The positioning of catalytic groups within proteins plays an important role in enzyme catalysis, and here we investigate the positioning of the general base in the enzyme ketosteroid isomerase (KSI). The oxygen atoms of Asp38, the general base in KSI, were previously shown to be involved in anion-aromatic interactions with two neighboring Phe residues. Here we ask whether those interactions are sufficient, within the overall protein architecture, to position Asp38 for catalysis or whether the side chains that pack against Asp38 and/or the residues of the structured loop that is capped by Asp38 are necessary to achieve optimal positioning for catalysis. To test positioning, we mutated each of the aforementioned residues, alone and in combinations, in a background with the native Asp general base and in a D38E mutant background, as Glu at position 38 was previously shown to be mispositioned for general base catalysis. These double-mutant cycles reveal positioning effects as large as 10(3)-fold, indicating that structural features in addition to the overall protein architecture and the Phe residues neighboring the carboxylate oxygen atoms play roles in positioning. X-ray crystallography and molecular dynamics simulations suggest that the functional effects arise from both restricting dynamic fluctuations and disfavoring potential mispositioned states. Whereas it may have been anticipated that multiple interactions would be necessary for optimal general base positioning, the energetic contributions from positioning and the nonadditive nature of these interactions are not revealed by structural inspection and require functional dissection. Recognizing the extent, type, and energetic interconnectivity of interactions that contribute to positioning catalytic groups has implications for enzyme evolution and may help reveal the nature and extent of interactions required to design enzymes that rival those found in biology.


Asunto(s)
Mutagénesis , Esteroide Isomerasas/metabolismo , Secuencia de Aminoácidos , Aminoácidos/metabolismo , Dominio Catalítico , Cristalografía por Rayos X , Interacciones Hidrofóbicas e Hidrofílicas , Cinética , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Esteroide Isomerasas/química
16.
Biochemistry ; 52(44): 7840-55, 2013 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-24151972

RESUMEN

Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.


Asunto(s)
Proteínas Bacterianas/química , Pseudomonas putida/enzimología , Esteroide Isomerasas/química , Tirosina/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Catálisis , Dominio Catalítico , Cristalografía por Rayos X , Enlace de Hidrógeno , Cetosteroides/química , Cetosteroides/metabolismo , Cinética , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Pseudomonas putida/genética , Pseudomonas putida/metabolismo , Esteroide Isomerasas/genética , Esteroide Isomerasas/metabolismo , Tirosina/genética , Tirosina/metabolismo
17.
Proc Natl Acad Sci U S A ; 110(28): E2552-61, 2013 Jul 09.
Artículo en Inglés | MEDLINE | ID: mdl-23798390

RESUMEN

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.


Asunto(s)
Cetosteroides/metabolismo , Protones , Esteroide Isomerasas/metabolismo , Dominio Catalítico , Enlace de Hidrógeno , Transporte Iónico , Modelos Moleculares , Pseudomonas putida/enzimología , Espectrofotometría Infrarroja
18.
Proc Natl Acad Sci U S A ; 110(28): 11308-13, 2013 Jul 09.
Artículo en Inglés | MEDLINE | ID: mdl-23798413

RESUMEN

Although the cation-pi pair, formed between a side chain or substrate cation and the negative electrostatic potential of a pi system on the face of an aromatic ring, has been widely discussed and has been shown to be important in protein structure and protein-ligand interactions, there has been little discussion of the potential structural and functional importance in proteins of the related anion-aromatic pair (i.e., interaction of a negatively charged group with the positive electrostatic potential on the ring edge of an aromatic group). We posited, based on prior structural information, that anion-aromatic interactions between the anionic Asp general base and Phe54 and Phe116 might be used instead of a hydrogen-bond network to position the general base in the active site of ketosteroid isomerase from Comamonas testosteroni as there are no neighboring hydrogen-bonding groups. We have tested the role of the Phe residues using site-directed mutagenesis, double-mutant cycles, and high-resolution X-ray crystallography. These results indicate a catalytic role of these Phe residues. Extensive analysis of the Protein Data Bank provides strong support for a catalytic role of these and other Phe residues in providing anion-aromatic interactions that position anionic general bases within enzyme active sites. Our results further reveal a potential selective advantage of Phe in certain situations, relative to more traditional hydrogen-bonding groups, because it can simultaneously aid in the binding of hydrophobic substrates and positioning of a neighboring general base.


Asunto(s)
Cetosteroides/metabolismo , Esteroide Isomerasas/metabolismo , Aniones , Dominio Catalítico , Mutación , Esteroide Isomerasas/química , Esteroide Isomerasas/genética , Difracción de Rayos X
19.
Biochemistry ; 52(6): 1074-81, 2013 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-23311398

RESUMEN

We compared the binding affinities of ground state analogues for bacterial ketosteroid isomerase (KSI) with a wild-type anionic Asp general base and with uncharged Asn and Ala in the general base position to provide a measure of potential ground state destabilization that could arise from the close juxtaposition of the anionic Asp and hydrophobic steroid in the reaction's Michaelis complex. The analogue binding affinity increased ~1 order of magnitude for the Asp38Asn mutation and ~2 orders of magnitude for the Asp38Ala mutation, relative to the affinity with Asp38, for KSI from two sources. The increased level of binding suggests that the abutment of a charged general base and a hydrophobic steroid is modestly destabilizing, relative to a standard state in water, and that this destabilization is relieved in the transition state and intermediate in which the charge on the general base has been neutralized because of proton abstraction. Stronger binding also arose from mutation of Pro39, the residue adjacent to the Asp general base, consistent with an ability of the Asp general base to now reorient to avoid the destabilizing interaction. Consistent with this model, the Pro mutants reduced or eliminated the increased level of binding upon replacement of Asp38 with Asn or Ala. These results, supported by additional structural observations, suggest that ground state destabilization from the negatively charged Asp38 general base provides a modest contribution to KSI catalysis. They also provide a clear illustration of the well-recognized concept that enzymes evolve for catalytic function and not, in general, to maximize ground state binding. This ground state destabilization mechanism may be common to the many enzymes with anionic side chains that deprotonate carbon acids.


Asunto(s)
Alanina/metabolismo , Asparagina/metabolismo , Ácido Aspártico/metabolismo , Comamonas testosteroni/enzimología , Pseudomonas putida/enzimología , Esteroide Isomerasas/química , Alanina/química , Alanina/genética , Asparagina/química , Asparagina/genética , Ácido Aspártico/química , Ácido Aspártico/genética , Sitios de Unión , Catálisis , Dominio Catalítico , Comamonas testosteroni/genética , Cristalografía por Rayos X , Enlace de Hidrógeno , Cetosteroides/metabolismo , Cinética , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Mutación/genética , Pseudomonas putida/genética , Esteroide Isomerasas/genética , Esteroide Isomerasas/metabolismo
20.
Proc Natl Acad Sci U S A ; 109(6): E299-308, 2012 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-22308339

RESUMEN

Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.


Asunto(s)
Dominio Catalítico , Pseudomonas putida/enzimología , Electricidad Estática , Esteroide Isomerasas/metabolismo , Absorción , Ácido Aspártico/metabolismo , Biocatálisis , Cristalografía por Rayos X , Concentración de Iones de Hidrógeno , Iones , Ligandos , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Sondas Moleculares/metabolismo , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Nitrilos/metabolismo , Espectrofotometría Ultravioleta , Espectroscopía Infrarroja por Transformada de Fourier , Esteroide Isomerasas/química , Volumetría , Tirosina/metabolismo , Vibración
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