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1.
Biol Chem ; 403(11-12): 1031-1042, 2022 Nov 25.
Article in English | MEDLINE | ID: mdl-36165459

ABSTRACT

Heme is a vital cofactor of proteins with roles in oxygen transport (e.g. hemoglobin), storage (e.g. myoglobin), and activation (e.g. P450) as well as electron transfer (e.g. cytochromes) and many other functions. However, its structural and functional role in oxygen sensing proteins differs markedly from that in most other enzymes, where it serves as a catalytic or functional center. This minireview discusses the mechanism of signal transduction in two heme-based oxygen sensors: the histidine kinase AfGcHK and the diguanylate cyclase YddV (EcDosC), both of which feature a heme-binding domain containing a globin fold resembling that of hemoglobin and myoglobin.


Subject(s)
Heme , Myoglobin , Histidine Kinase/chemistry , Histidine Kinase/metabolism , Heme/chemistry , Myoglobin/metabolism , Oxygen/metabolism , Signal Transduction , Hemoglobins
2.
Clin Auton Res ; 32(1): 9-17, 2022 02.
Article in English | MEDLINE | ID: mdl-34997877

ABSTRACT

INTRODUCTION: Takotsubo syndrome (TTS), also known as stress cardiomyopathy or "broken heart" syndrome, is a mysterious condition that often mimics an acute myocardial infarction. Both are characterized by left ventricular systolic dysfunction. However, this dysfunction is reversible in the majority of TTS patients. PURPOSE: Recent studies surprisingly demonstrated that TTS, initially perceived as a benign condition, has a long-term prognosis akin to myocardial infarction. Therefore, the health consequences and societal impact of TTS are not trivial. The pathophysiological mechanisms of TTS are not yet completely understood. In the last decade, attention has been increasingly focused on the putative role of the central nervous system in the pathogenesis of TTS. CONCLUSION: In this review, we aim to summarize the state of the art in the field of the brain-heart axis, regional structural and functional brain abnormalities, and connectivity aberrancies in TTS.


Subject(s)
Takotsubo Cardiomyopathy , Autonomic Nervous System , Brain , Humans , Prognosis , Takotsubo Cardiomyopathy/etiology
3.
Vnitr Lek ; 67(7): 433-437, 2021.
Article in English | MEDLINE | ID: mdl-35459362

ABSTRACT

Contrast induced nephropathy is associated with worse clinical outcome in patients undergoing coronary intervention. The most profound risk factor is advanced chronic renal insufficiency. Due to the increasing number of coronary interventions on severally ill patients, there is a need of modern therapeutic approach that could reduce the volume of contrast media to minimum or even zero. Herein, the authors present a case report of a 68-year-old patient with chronic kidney disease, who required elective coronary intervention (PCI) due to a significant lesion of the left anterior descending coronary artery. During this intervention, maximum emphasis was given on reduction of contrast media. To the best of our knowledge, this was the first similar intervention performed in the Czech Republic. Minimum contrast PCI guided by the intracoronary ultrasound, i.e. the IVUS-guided zero-contrast PCI may serve as a potential alternative to standard, angiography-guided PCI.


Subject(s)
Coronary Artery Disease , Percutaneous Coronary Intervention , Renal Insufficiency, Chronic , Aged , Contrast Media/adverse effects , Coronary Angiography , Coronary Artery Disease/diagnostic imaging , Coronary Artery Disease/surgery , Czech Republic , Female , Humans , Male , Percutaneous Coronary Intervention/adverse effects , Renal Insufficiency, Chronic/complications , Treatment Outcome , Ultrasonography, Interventional
4.
Vnitr Lek ; 66(6): 378-380, 2020.
Article in English | MEDLINE | ID: mdl-33380143

ABSTRACT

Takotsubo or broken heart syndrome represents a rare type of cardiomyopathy, often imitating acute myocardial infarction. It is a sudden transient cardiac syndrome that typically involves left ventricular apical akinesis with preserved motility of basal heart segments. In contrast to acute myocardial infarction, the pathology is fully reversible in the majority of patients. In the present casereport, we discuss 78yearsold female referred to our department for typical symptomatology of acute myocardial infarction. Coronary angiography revealed significant stenosis on the left anterior descending coronary artery, but ventriculography disclosed apical dysfunction and clinical course of the disease result in the diagnosis of Takotsubo cardiomyopathy. Until recently, normal or nonobstructive coronary angiography represented one of the mean diagnostic features of Takotsubo cardiomyopathy. In 2018, new diagnostic criteria were introduced, importantly modifying our approach to the Takotsubo diagnostics with omitting a coronary lesion as an exclusion criterium of the Takotsubo cardiomyopathy.


Subject(s)
Myocardial Infarction , Takotsubo Cardiomyopathy , Coronary Angiography , Diagnosis, Differential , Electrocardiography , Female , Humans , Myocardial Infarction/diagnostic imaging , Takotsubo Cardiomyopathy/diagnostic imaging
5.
PLoS One ; 12(10): e0185404, 2017.
Article in English | MEDLINE | ID: mdl-29016632

ABSTRACT

AIMS: Transradial catheterization (TRC) is a dominant access site for coronary catheterization and percutaneous coronary interventions (PCI) in many centers. Previous studies reported higher intimal thickness of the radial artery (RA) wall in patients with a previous history of TRC. In this investigation the aim was to assess the intimal changes of RA using the optical coherence tomography (OCT) intravascular imaging in a serial manner. METHODS AND RESULTS: 100 patients with the diagnosis of non-ST-elevation myocardial infarction (nSTEMI) treated by PCI were enrolled (6 patients were excluded from this analysis because of occluded RA at follow-up [2 patients] and insufficient quality of OCT images [4 patients]). An 54mm long OCT run of the RA was performed immediately after the index PCI and repeated 9 months later. Volumetric analyses of the intimal layer and lumen changes were conducted. Median intimal volume at baseline versus 9 months was 33.9mm3 (19.0; 69.4) versus 39.0mm3 (21.7; 72.6) (p<0.001); and median arterial lumen volume was 356.3mm3 (227.8; 645.3) versus 304.7mm3 (186.1; 582.7) (p<0.001). There was no significant difference in the effect of any clinical factor on the RA volume changes. CONCLUSIONS: OCT volumetric analyses at baseline and 9 months showed a significant increase in the radial artery intimal layer volume and a decrease in lumen volume after transradial PCI. No significant factors affecting this process were identified.


Subject(s)
Cardiac Catheterization/adverse effects , Myocardial Infarction/therapy , Percutaneous Coronary Intervention/adverse effects , Tomography, Optical Coherence , Aged , Aged, 80 and over , Coronary Angiography/adverse effects , Coronary Angiography/methods , Female , Humans , Hyperplasia/diagnostic imaging , Hyperplasia/etiology , Hyperplasia/physiopathology , Male , Middle Aged , Myocardial Infarction/diagnostic imaging , Myocardial Infarction/physiopathology , Neointima/diagnostic imaging , Neointima/physiopathology , Radial Artery/diagnostic imaging , Radial Artery/physiopathology , Tunica Intima/diagnostic imaging , Tunica Intima/physiopathology
6.
Phys Chem Chem Phys ; 18(44): 30344-30356, 2016 Nov 09.
Article in English | MEDLINE | ID: mdl-27722524

ABSTRACT

Cytochrome P450 1A2 (P450 1A2, CYP1A2) is a membrane-bound enzyme that oxidizes a broad range of hydrophobic substrates. The structure and dynamics of both the catalytic and trans-membrane (TM) domains of this enzyme in the membrane/water environment were investigated using a multiscale computational approach, including coarse-grained and all-atom molecular dynamics. Starting from the spontaneous self-assembly of the system containing the TM or soluble domain immersed in randomized dilauroyl phosphatidylcholine (DLPC)/water mixture into their respective membrane-bound forms, we reconstituted the membrane-bound structure of the full-length P450 1A2. This structure includes a TM helix that spans the membrane, while being connected to the catalytic domain by a short flexible loop. Furthermore, in this model, the upper part of the TM helix interacts directly with a conserved and highly hydrophobic N-terminal proline-rich segment of the catalytic domain; this segment and the FG loop are immersed in the membrane, whereas the remaining portion of the catalytic domain remains exposed to aqueous solution. The shallow membrane immersion of the catalytic domain induces a depression in the opposite intact layer of the phospholipids. This structural effect may help in stabilizing the position of the TM helix directly beneath the catalytic domain. The partial immersion of the catalytic domain also allows for the enzyme substrates to enter the active site from either aqueous solution or phospholipid environment via several solvent- and membrane-facing tunnels in the full-length P450 1A2. The calculated tunnel dynamics indicated that the opening probability of the membrane-facing tunnels is significantly enhanced when a DLPC molecule spontaneously penetrates into the membrane-facing tunnel 2d. The energetics of the lipid penetration process were assessed by the linear interaction energy (LIE) approximation, and found to be thermodynamically feasible.


Subject(s)
Cytochrome P-450 CYP1A2/chemistry , Phospholipids/chemistry , Animals , Catalysis , Catalytic Domain , Humans , Molecular Dynamics Simulation , Phosphatidylcholines , Protein Binding
7.
Article in English | MEDLINE | ID: mdl-27641357

ABSTRACT

BACKGROUND AND AIMS: Transradial catheterization is the predominant access site for coronary catheterization and percutaneous coronary interventions (PCI). Previous studies have reported a high incidence of radial artery (RA) injury. The aim of this investigation was to evaluate the incidence of RA injury using last generation optical coherence tomography (OCT) intravascular imaging in a serial manner. METHODS: 100 patients with a diagnosis of non-ST-elevation myocardial infarction (nSTEMI) treated by PCI were enrolled. OCT of RA was performed immediately after the index PCI. OCT was repeated 9 months later. RESULTS: There were 11 patients with RA injuries (11.0%) at baseline, including 3 patients with RA medial dissection and 8 patients with intimal tears. In the follow-up OCT data, the number of RA injuries was 10 (10.0%), including 7 patients with RA medial dissection and 3 patients with intimal tear. All injuries were clinically asymptomatic and there was no finding of vessel perforation. There was no significant difference between the baseline and follow-up procedure in terms of number of injuries. CONCLUSION: The study showed no significant difference between baseline and follow-up RA injury incidence. There was a higher risk of radial injury for repeated catheterization in women. The conclusion is that radial catheterization is a very safe procedure in terms of radial artery damage. This is evidenced by considerably fewer injuries compared to published studies. The use of the short radial sheath (7 cm in this study) is protective and reduces the incidence of radial injury.


Subject(s)
Percutaneous Coronary Intervention/adverse effects , Radial Artery/injuries , Adult , Aged , Coronary Angiography , Female , Humans , Intraoperative Complications/diagnostic imaging , Intraoperative Complications/etiology , Male , Middle Aged , Prospective Studies , Radial Artery/diagnostic imaging , ST Elevation Myocardial Infarction/surgery , Tomography, Optical Coherence/methods
8.
Int J Cardiol ; 214: 235-40, 2016 Jul 01.
Article in English | MEDLINE | ID: mdl-27077540

ABSTRACT

BACKGROUND: We compared the prognostic capacity of conventional and novel invasive parameters derived from the slope of the preload recruitable stroke work relationship (PRSW) in STEMI patients and assessed their contribution to the TIMI risk score. METHODS: Left ventricular end-diastolic pressure (EDP), ejection fraction (EF), pressure adjusted maximum rate of pressure change in the left ventricle (dP/dt/P), aortic systolic pressure to EDP ratio (SBP/EDP) and end-diastolic volume adjusted stroke work (EW), derived from the slope of the PRSW relationship, were obtained during the emergency cardiac catheterization in 523 STEMI patients. The predictive power of the analyzed parameters for 30-day and 1-year mortality was evaluated using C-statistics and reclassification analysis was adopted to assess the improvement in TIMI score. RESULTS: The highest area under the curve (AUC) values for 30-day mortality were observed for EW (0.872(95% confidence interval 0.801-0.943)), SBP/EDP (0.843(0.758-0.928)) and EF (0.833(0.735-0.931)); p<0.001 for all values. For 1-year mortality the best predictive value was found for EW (0.806(0.724-0.887) and EF (0.793(0.703-0.883)); p<0.001 for both. The addition of EDP, SBP/EDP ratio and EW to TIMI score significantly increased the AUC according to De Long's test. For 30-day mortality, increased discriminative power following addition to the TIMI score was observed for EW and SBP/EDP (Integrated Discrimination Improvement was 0.086(0.033-0.140), p=0.002 and 0.078(0.028-0.128), p=0.002, respectively). CONCLUSIONS: EW and SBP/EDP are prognostic markers with high predictive value for 30-day and 1-year mortality. Both parameters, easily obtained during emergency catheterization, improve the discriminatory capacity of the TIMI score for 30-day mortality.


Subject(s)
ST Elevation Myocardial Infarction/diagnosis , Aged , Aged, 80 and over , Female , Hemodynamics , Humans , Male , Middle Aged , Predictive Value of Tests , Prognosis , Risk Assessment , ST Elevation Myocardial Infarction/mortality , ST Elevation Myocardial Infarction/physiopathology , Stroke Volume/physiology
9.
Chem Res Toxicol ; 29(4): 626-36, 2016 Apr 18.
Article in English | MEDLINE | ID: mdl-26918755

ABSTRACT

Eukaryotic cytochromes P450 (P450) are membrane-bound enzymes oxidizing a broad spectrum of hydrophobic substrates, including xenobiotics. Protein-protein interactions play a critical role in this process. In particular, the formation of transient complexes of P450 with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates catalytic activities of several P450s. To lay a structural foundation for the investigation of these effects, we constructed a model of the membrane-bound full-length human P450 1A2-cyt b5 complex. The model was assembled from several parts using a multiscale modeling approach covering all-atom and coarse-grained molecular dynamics (MD). For soluble P450 1A2-cyt b5 complexes, these simulations yielded three stable binding modes (sAI, sAII, and sB). The membrane-spanning transmembrane domains were reconstituted with the phospholipid bilayer using self-assembly MD. The predicted full-length membrane-bound complexes (mAI and mB) featured a spontaneously formed X-shaped contact between antiparallel transmembrane domains, whereas the mAII mode was found to be unstable in the membrane environment. The mutual position of soluble domains in binding mode mAI was analogous to the sAI complex. Featuring the largest contact area, the least structural flexibility, the shortest electron transfer distance, and the highest number of interprotein salt bridges, mode mAI is the best candidate for the catalytically relevant full-length complex.


Subject(s)
Cytochrome P-450 CYP1A2/metabolism , Cytochromes b5/metabolism , Cytochrome P-450 CYP1A2/chemistry , Cytochromes b5/chemistry , Humans , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Molecular Dynamics Simulation , Phospholipids/chemistry , Phospholipids/metabolism , Protein Binding , Protein Domains , Protein Structure, Secondary
10.
Neuro Endocrinol Lett ; 36 Suppl 1: 29-37, 2015.
Article in English | MEDLINE | ID: mdl-26757119

ABSTRACT

OBJECTIVES: Cytochromes P450 (CYPs) are heme enzymes oxygenating a broad range of substrates. Their activity is dependent on the presence of a suitable electron donor (eukaryotic NADPH:CYP oxidoreductase or cytochrome b5). The Escherichia naturally contain no CYPs and no NADPH:CYP oxidoreductase, however it was reported that some CYPs heterologously expressed in E. coli may exist in the ferrous form. A small bacterial flavoprotein, flavodoxin is considered to be responsible for reduction some of these CYPs. METHODS: The reduction state of several human CYPs expressed in the intact living E. coli cells was examined. In addition, molecular dynamics and steered molecular dynamics simulations were performed to predict and compare affinity of flavodoxin toward selected CYPs. RESULTS: We determined the reduction state of five human CYPs heterologously expressed in E. coli. The computationally predicted stabilities of CYP-flavodoxin complexes correlate with the percentage of reduced CYPs in bacterial cells. The mean electron transfer distance within optimized complexes was also related to the percentage of reduced CYPs. CONCLUSION: Depending on the resting state, the CYPs heterologously expressed in E. coli could be divided into two groups; CYP2C8, 2C9, 3A4 are in E. coli present mainly in the oxidized form; while CYP1A1, 1A2, 2A6, 2A13, 2B6, 2D6 are found predominantly in the reduced form. We found a significant correlation between the stability of CYP-flavodoxin complexes and the percentage of reduced CYPs in bacteria. Hence, the naturally expressed flavodoxin is probably responsible for reduction of a larger group of human CYPs in bacterial cells.


Subject(s)
Cytochrome P-450 Enzyme System/metabolism , Ferric Compounds/metabolism , Ferrous Compounds/metabolism , Flavodoxin/metabolism , NADPH-Ferrihemoprotein Reductase/metabolism , Aryl Hydrocarbon Hydroxylases/metabolism , Cytochrome P-450 CYP1A1/metabolism , Cytochrome P-450 CYP1A2/metabolism , Cytochrome P-450 CYP2A6/metabolism , Cytochrome P-450 CYP2B6/metabolism , Cytochrome P-450 CYP2C8/metabolism , Cytochrome P-450 CYP2C9/metabolism , Cytochrome P-450 CYP2D6/metabolism , Cytochrome P-450 CYP3A/metabolism , Escherichia coli , Humans , Organisms, Genetically Modified , Oxidation-Reduction
11.
Biochemistry ; 53(42): 6695-705, 2014 Oct 28.
Article in English | MEDLINE | ID: mdl-25313797

ABSTRACT

Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.


Subject(s)
Cytochrome P-450 CYP1A2/chemistry , Cytochromes b5/chemistry , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Conformation , Static Electricity
12.
Vnitr Lek ; 60(5-6): 531-4, 2014.
Article in Czech | MEDLINE | ID: mdl-24974760

ABSTRACT

Acute coronary syndrome may develop in the background of hemodynamically non-significant coronary artery disease. It may be caused by the presence of "vulnerable plaque", which is characterized by the lipid rich core and thin fibrous cap content. NIRS - near infrared spectroscopy - is a morphological imaging method allowing determining atherosclerotic plaque cholesterol burden. Information about the chemical composition may contribute to "high risk" plaque early identification and subsequent optimal interventional strategy. The first experience with the clinical implementation of this novel method is demonstrated in a case report. Key words: acute coronary syndrome - chemogram - intravascular imaging - NIRS - vulnerable plaque.


Subject(s)
Acute Coronary Syndrome/diagnostic imaging , Plaque, Atherosclerotic/diagnostic imaging , Adult , Diagnosis, Differential , Female , Humans , Radiography , Spectroscopy, Near-Infrared
13.
Biochemistry ; 51(44): 8829-43, 2012 Nov 06.
Article in English | MEDLINE | ID: mdl-23013478

ABSTRACT

We carried out free-energy calculations and transient kinetic experiments for the insertion of the right (dC) and wrong (dA) nucleotides by wild-type (WT) and six mutant variants of human DNA polymerase ß (Pol ß). Since the mutated residues in the point mutants, I174S, I260Q, M282L, H285D, E288K, and K289M, were not located in the Pol ß catalytic site, we assumed that the WT and its point mutants share the same dianionic phosphorane transition-state structure of the triphosphate moiety of deoxyribonucleotide 5'-triphosphate (dNTP) substrate. On the basis of this assumption, we have formulated a thermodynamic cycle for calculating relative dNTP insertion efficiencies, Ω = (k(pol)/K(D))(mut)/(k(pol)/K(D))(WT) using free-energy perturbation (FEP) and linear interaction energy (LIE) methods. Kinetic studies on five of the mutants have been published previously using different experimental conditions, e.g., primer-template sequences. We have performed a presteady kinetic analysis for the six mutants for comparison with wild-type Pol ß using the same conditions, including the same primer/template DNA sequence proximal to the dNTP insertion site used for X-ray crystallographic studies. This consistent set of kinetic and structural data allowed us to eliminate the DNA sequence from the list of factors that can adversely affect calculated Ω values. The calculations using the FEP free energies scaled by 0.5 yielded 0.9 and 1.1 standard deviations from the experimental log Ω values for the insertion of the right and wrong dNTP, respectively. We examined a hybrid FEP/LIE method in which the FEP van der Waals term for the interaction of the mutated amino acid residue with its surrounding environment was replaced by the corresponding van der Waals term calculated using the LIE method, resulting in improved 0.4 and 1.0 standard deviations from the experimental log Ω values. These scaled FEP and FEP/LIE methods were also used to predict log Ω for R283A and R283L Pol ß mutants.


Subject(s)
DNA Polymerase beta/chemistry , DNA Polymerase beta/genetics , Amino Acid Sequence , Amino Acid Substitution , Base Sequence , Catalysis , Deoxyribonucleotides/genetics , Deoxyribonucleotides/metabolism , Humans , Kinetics , Molecular Dynamics Simulation , Point Mutation , Thermodynamics
14.
Neuro Endocrinol Lett ; 33 Suppl 3: 25-32, 2012.
Article in English | MEDLINE | ID: mdl-23353840

ABSTRACT

OBJECTIVES: The herbal drug aristolochic acid (AA) derived from Aristolochia species has been shown to be the cause of aristolochic acid nephropathy (AAN), Balkan endemic nephropathy (BEN) and their urothelial malignancies. One of the common features of AAN and BEN is that not all individuals exposed to AA suffer from nephropathy and tumor development. One cause for these different responses may be individual differences in the activities of the enzymes catalyzing the biotransformation of AA. Thus, the identification of enzymes principally involved in the metabolism of AAI, the major toxic component of AA, and detailed knowledge of their catalytic specificities is of major importance. Human cytochrome P450 (CYP) 1A1 and 1A2 enzymes were found to be responsible for the AAI reductive activation to form AAI-DNA adducts, while its structurally related analogue, CYP1B1 is almost without such activity. However, knowledge of the differences in mechanistic details of CYP1A1-, 1A2-, and 1B1- mediated reduction is still lacking. Therefore, this feature is the aim of the present study. METHODS: Molecular modeling capable of evaluating interactions of AAI with the active site of human CYP1A1, 1A2 and 1B1 under the reductive conditions was used. In silico docking, employing soft-soft (flexible) docking procedure was used to study the interactions of AAI with the active sites of these human enzymes. RESULTS: The predicted binding free energies and distances between an AAI ligand and a heme cofactor are similar for all CYPs evaluated. AAI also binds to the active sites of CYP1A1, 1A2 and 1B1 in similar orientations. The carboxylic group of AAI is in the binding position situated directly above heme iron. This ligand orientation is in CYP1A1/1A2 further stabilized by two hydrogen bonds; one between an oxygen atom of the AAI nitro-group and the hydroxyl group of Ser122/Thr124; and the second bond between an oxygen atom of dioxolane ring of AAI and the hydroxyl group of Thr497/Thr498. For the CYP1B1:AAI complex, however, any hydrogen bonding of the nitro-group of AAI is prevented as Ser122/Thr124 residues are in CYP1B1 protein replaced by hydrophobic residue Ala133. CONCLUSION: The experimental observations indicate that CYP1B1 is more than 10× less efficient in reductive activation of AAI than CYP1A2. The docking simulation however predicts the binding pose and binding energy of AAI in the CYP1B1 pocket to be analogous to that found in CYP1A1/2. We believe that the hydroxyl group of S122/T124 residue, with its polar hydrogen placed close to the nitro group of the substrate (AAI), is mechanistically important, for example it could provide a proton required for the stepwise reduction process. The absence of a suitable proton donor in the AAI-CYP1B1 binary complex could be the key difference, as the nitro group is in this complex surrounded only by the hydrophobic residues with potential hydrogen donors not closer than 5 Å.


Subject(s)
Aristolochic Acids/adverse effects , Aristolochic Acids/pharmacokinetics , Aryl Hydrocarbon Hydroxylases/metabolism , Cytochrome P-450 CYP1A1/metabolism , Cytochrome P-450 CYP1A2/metabolism , Amino Acid Sequence , Aristolochia/chemistry , Aristolochic Acids/chemistry , Aryl Hydrocarbon Hydroxylases/chemistry , Aryl Hydrocarbon Hydroxylases/genetics , Catalytic Domain/drug effects , Computer Simulation , Cytochrome P-450 CYP1A1/chemistry , Cytochrome P-450 CYP1A1/genetics , Cytochrome P-450 CYP1A2/chemistry , Cytochrome P-450 CYP1A2/genetics , Cytochrome P-450 CYP1B1 , DNA Adducts/chemistry , DNA Adducts/metabolism , Drugs, Chinese Herbal/adverse effects , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/pharmacokinetics , Humans , Hydrogen Bonding/drug effects , Hydrophobic and Hydrophilic Interactions/drug effects , Kidney Diseases/chemically induced , Models, Chemical , Molecular Sequence Data , Nitroreductases/adverse effects , Nitroreductases/chemistry , Nitroreductases/pharmacokinetics , Protein Structure, Tertiary/drug effects
15.
Biochemistry ; 50(32): 7023-32, 2011 Aug 16.
Article in English | MEDLINE | ID: mdl-21739967

ABSTRACT

We show how a restricted reaction surface can be used to facilitate the calculation of biologically important contributions of active site geometries and dynamics to DNA polymerase fidelity. Our analysis, using human DNA polymerase beta (pol ß), is performed within the framework of an electrostatic linear free energy response (EFER) model. The structure, dynamics, and energetics of pol ß-DNA-dNTP interactions are computed between two points on the multidimensional reaction free energy surface. "Point 1" represents a ground state activation intermediate (GSA), which is obtained by deprotonating the terminal 3'OH group of the primer DNA strand. "Point 2" is the transition state (PTS) for the attack of the 3'O(-) (O(nuc)) on the P(α) atom of dNTP substrate, having the electron density of a dianionic phosphorane intermediate. Classical molecular dynamics simulations are used to compute the geometric and dynamic contributions to the formation of right and wrong O(nuc)-P chemical bonds. Matched dCTP·G and mismatched dATP·G base pairs are used to illustrate the analysis. Compared to the dCTP·G base pair, the dATP·G mismatch has fewer GSA configurations with short distances between O(nuc) and P(α) atoms and between the oxygen in the scissile P-O bond (O(lg)) and the nearest structural water. The thumb subdomain conformation of the GSA complex is more open for the mismatch, and the H-bonds in the mispair become more extended during the nucleophilic attack than in the correct pair. The electrostatic contributions of pol ß and DNA residues to catalysis of the right and wrong P-O(nuc) bond formation are 5.3 and 3.1 kcal/mol, respectively, resulting in an 80-fold contribution to fidelity. The EFER calculations illustrate the considerable importance of Arg183 and an O(lg)-proximal water molecule to pol ß fidelity.


Subject(s)
DNA Polymerase beta/chemistry , Models, Molecular , Base Pairing , DNA/chemistry , Humans , Water/chemistry
17.
FEBS J ; 275(24): 6123-35, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19016858

ABSTRACT

Beta-glucosidases such as Zm-p60.1 (Zea mays) and Bgl4:1 (Brassica napus) have implicated roles in regulating plant development by releasing biologically active cytokinins from O-glucosides. A key determinant of substrate specificity in Zm-p60.1 is the F193-F200-W373-F461 cluster. However, despite sharing the same substrates, amino acids in the active sites of Zm-p60.1 and Bgl4:1 differ dramatically. In members of the Brassicaceae we found a group of beta-glucosidases sharing both high similarity to Bgl4:1 and a consensus motif A-K-K-L corresponding to the F193-F200-W373-F461 cluster. To study the mechanism of substrate specificity further, we generated and analyzed four single (F193A, F200K, W373K and F461L) and one quadruple (F193A-F200K-W373K-F461L) mutants of Zm-p60.1. The F193A mutant showed a specific increase in affinity for a small polar aglycone, and a deep decrease in k(cat) compared with the wild-type. Formation of a cavity with decreased hydrophobicity, and significant consequent alterations in ratios of reactive and non-reactive complexes, revealed by computer modeling, may explain the observed changes in kinetic parameters of the F193 mutant. The large decrease in k(cat) for the W373K mutant was unexpected, but the findings are consistent with the F193-aglycone-W373 interaction playing a dual role in the enzyme's catalytic action; influencing both substrate specificity, and the catalytic rate by fixing the glucosidic bond in a favorable orientation for attack by the catalytic pair. Investigation of the combined effects of all of the mutations in the quadruple mutant of Zm-p60.1 was precluded by extensive alterations in its structure and almost complete abolition of its enzymatic activity.


Subject(s)
Plant Proteins/metabolism , Zea mays/enzymology , beta-Glucosidase/metabolism , Amino Acids/analysis , Binding Sites , Brassica napus/enzymology , Catalytic Domain , Escherichia coli/enzymology , Escherichia coli/genetics , Kinetics , Models, Molecular , Phylogeny , Plant Proteins/chemistry , Plant Proteins/classification , Plants/classification , Plants/enzymology , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Substrate Specificity , beta-Glucosidase/chemistry
18.
J Comput Aided Mol Des ; 20(6): 375-83, 2006 Jun.
Article in English | MEDLINE | ID: mdl-17016745

ABSTRACT

1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from Rhodococcus sp. hydrolyses the carbon-halogen bond in various halogenated compounds including TCP, but with low efficiency (k (cat)/K (m )= 36 s(-1) M(-1)). A Cys176Tyr-DhaA mutant with a threefold higher catalytic efficiency for TCP dehalogenation has been previously obtained by error-prone PCR. We have used molecular simulations and quantum mechanical calculations to elucidate the molecular mechanisms involved in the improved catalysis of the mutant, and enantioselectivity of DhaA toward TCP. The Cys176Tyr mutation modifies the protein access and export routes. Substitution of the Cys residue by the bulkier Tyr narrows the upper tunnel, making the second tunnel "slot" the preferred route. TCP can adopt two major orientations in the DhaA enzyme, in one of which the halide-stabilizing residue Asn41 forms a hydrogen bond with the terminal halogen atom of the TCP molecule, while in the other it bonds with the central halogen atom. The differences in these binding patterns explain the preferential formation of the (R)- over the (S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction catalyzed by the enzyme.


Subject(s)
Hydrolases/metabolism , Models, Molecular , Propane/analogs & derivatives , Hydrolases/genetics , Mutation , Polymerase Chain Reaction , Propane/chemistry
19.
Appl Environ Microbiol ; 71(4): 2183-5, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15812056

ABSTRACT

Beta-Hexachlorocyclohexane (beta-HCH) is the most recalcitrant among the alpha-, beta-, gamma-, and delta-isomers of HCH and causes serious environmental pollution problems. We demonstrate here that the haloalkane dehalogenase LinB, reported earlier to mediate the second step in the degradation of gamma-HCH in Sphingomonas paucimobilis UT26, metabolizes beta-HCH to produce 2,3,4,5,6-pentachlorocyclohexanol.


Subject(s)
Cyclohexanols/metabolism , Hexachlorocyclohexane/metabolism , Hydrolases/metabolism , Sphingomonas/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biodegradation, Environmental , Gene Expression Regulation, Bacterial , Hydrolases/genetics , Sphingomonas/genetics
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