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Methods in Enzymology 2016The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate... (Review)
Review
The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). We found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. We found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics.
Topics: Alcohol Dehydrogenase; Algorithms; Humans; Kinetics; L-Lactate Dehydrogenase; Mathematical Computing; Molecular Dynamics Simulation; Myocardium; Protons; Quantum Theory; Saccharomyces cerevisiae; Thermodynamics
PubMed: 27497161
DOI: 10.1016/bs.mie.2016.05.028 -
Magyar Onkologia Mar 2018Regular consumption of alcohol increases the risk of developing (one or more of) several malignant conditions: the frequency of tumours in the aerodigestive tract, in... (Review)
Review
Regular consumption of alcohol increases the risk of developing (one or more of) several malignant conditions: the frequency of tumours in the aerodigestive tract, in the liver, in the colorectal region and in the breast is increased. The principal carcinogen component of alcoholic drinks is ethanol itself; the effect is unmistakably proportional to the daily/weekly dosage. Under the influence of alcohol-dehydrogenase, ethanol will metabolise to acetaldehyde, which is a known carcinogen. Among other things chronic alcohol consumption promotes the production of endogen hormones, affects the insulin-like growth factor-1, alters several biological pathways, raises oxidative stress, and damages the genes. Even modest daily alcohol intake will increase the risk of breast cancer.
Topics: Acetaldehyde; Alcohol Dehydrogenase; Alcohol Drinking; Breast Neoplasms; Carcinogens; DNA Damage; Ethanol; Humans; Oxidative Stress
PubMed: 29570189
DOI: No ID Found -
Archives of Biochemistry and Biophysics Apr 2021Enzymes typically have high specificity for their substrates, but the structures of substrates and products differ, and multiple modes of binding are observed. In this...
Enzymes typically have high specificity for their substrates, but the structures of substrates and products differ, and multiple modes of binding are observed. In this study, high resolution X-ray crystallography of complexes with NADH and alcohols show alternative modes of binding in the active site. Enzyme crystallized with the good substrates NAD and 4-methylbenzyl alcohol was found to be an abortive complex of NADH with 4-methylbenzyl alcohol rotated to a "non-productive" mode as compared to the structures that resemble reactive Michaelis complexes with NAD and 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol. The NADH is formed by reduction of the NAD with the alcohol during the crystallization. The same structure was also formed by directly crystallizing the enzyme with NADH and 4-methylbenzyl alcohol. Crystals prepared with NAD and 4-bromobenzyl alcohol also form the abortive complex with NADH. Surprisingly, crystals prepared with NAD and the strong inhibitor 1H,1H-heptafluorobutanol also had NADH, and the alcohol was bound in two different conformations that illustrate binding flexibility. Oxidation of 2-methyl-2,4-pentanediol during the crystallization apparently led to reduction of the NAD. Kinetic studies show that high concentrations of alcohols can bind to the enzyme-NADH complex and activate or inhibit the enzyme. Together with previous studies on complexes with NADH and formamide analogues of the carbonyl substrates, models for the Michaelis complexes with NAD-alcohol and NADH-aldehyde are proposed.
Topics: Alcohol Dehydrogenase; Alcohols; Animals; Binding Sites; Catalytic Domain; Crystallography, X-Ray; Horses; Liver; Models, Chemical; NAD
PubMed: 33675814
DOI: 10.1016/j.abb.2021.108825 -
The American Journal on Addictions Sep 2022Discrimination due to race and/or ethnicity can be a pervasive stressor for Black college students in the United States beyond general negative life events and has...
BACKGROUND AND OBJECTIVES
Discrimination due to race and/or ethnicity can be a pervasive stressor for Black college students in the United States beyond general negative life events and has demonstrated associations with adverse health and alcohol outcomes. Genetics may confer individual differences in the risk of drinking to cope with discrimination-related stress. This study tested whether associations of racial/ethnic discrimination with coping drinking motives and alcohol use differ as a function of a well-documented variant in the alcohol dehydrogenase 1B gene (ADH1B*3).
METHODS
Cross-sectional data were obtained from 241 Black students (M = 20.04 [range = 18-53]; 66% female) attending a predominantly White university in the northeastern United States. Participants provided a saliva sample for genotyping and self-reported on their racial/ethnic discrimination experiences, coping drinking motives, and past-month total alcohol quantity.
RESULTS
Path models demonstrated that associations of discrimination with alcohol quantity directly or indirectly through coping drinking motives did not differ as a function of ADH1B*3, after controlling for gender, age, negative life events, and potential confounding interactions of covariates with model predictors. Regardless of ADH1B*3, greater experience of negative life events was associated with higher coping drinking motives, which in turn were associated with greater alcohol quantity. CONCLUSION AND SCIENTIFIC SIGNIFICANCE: Findings represent a novel investigation into gene-environment interplay in associations of alcohol use with racial/ethnic discrimination. Findings demonstrate coping-motivated drinking associated with negative life events within Black college drinkers regardless of ADH1B*3. Future research should leverage longitudinal designs to characterize associations of genetics, stressful experiences, and coping-motivated drinking over time.
Topics: Adaptation, Psychological; Adolescent; Adult; Alcohol Dehydrogenase; Alcohol Drinking; Alcohol Drinking in College; Cross-Sectional Studies; Ethnicity; Female; Humans; Male; Middle Aged; Motivation; Students; United States; Universities; Young Adult
PubMed: 35748313
DOI: 10.1111/ajad.13306 -
Biomolecules May 2023In our recent article (Smędra et al.: Oral form of auto-brewery syndrome. J Forensic Leg Med. 2022; 87: 102333), we showed that alcohol production can occur in the oral... (Review)
Review
In our recent article (Smędra et al.: Oral form of auto-brewery syndrome. J Forensic Leg Med. 2022; 87: 102333), we showed that alcohol production can occur in the oral cavity (oral auto-brewery syndrome) due to a disruption in the microbiota (dysbiosis). An intermediate step on the path leading to the formation of alcohol is acetaldehyde. Typically, acetic aldehyde is transformed into acetate particles inside the human body via acetaldehyde dehydrogenase. Unfortunately, acetaldehyde dehydrogenase activity is low in the oral cavity, and acetaldehyde remains there for a long time. Since acetaldehyde is a recognised risk factor for squamous cell carcinoma arising from the oral cavity, we decided to analyse the relationship linking the oral microbiome, alcohol, and oral cancer using the narrative review method, based on browsing articles in the PubMed database. In conclusion, enough evidence supports the speculation that oral alcohol metabolism must be assessed as an independent carcinogenic risk. We also hypothesise that dysbiosis and the production of acetaldehyde from non-alcoholic food and drinks should be treated as a new factor for the development of cancer.
Topics: Humans; Aldehyde Dehydrogenase; Dysbiosis; Mouth Neoplasms; Ethanol; Acetaldehyde; Microbiota; Alcohol Dehydrogenase
PubMed: 37238685
DOI: 10.3390/biom13050815 -
Biological Psychiatry Apr 2020Alcohol use disorder (AUD) is defined by several symptom criteria, which can be dissected further at the genetic level. Over the past several years, our understanding of... (Review)
Review
Alcohol use disorder (AUD) is defined by several symptom criteria, which can be dissected further at the genetic level. Over the past several years, our understanding of the genetic factors influencing alcohol use and abuse has progressed tremendously; numerous loci have been implicated in different aspects of alcohol use. Previously known associations with alcohol-metabolizing enzymes (ADH1B, ALDH2) have been replicated definitively. In addition, novel associations with loci containing the genes KLB, GCKR, CRHR1, and CADM2 have been reported. Downstream analyses have leveraged these genetic findings to reveal important relationships between alcohol use behaviors and both physical and mental health. AUD and aspects of alcohol misuse have been shown to overlap strongly with psychiatric disorders, whereas aspects of alcohol consumption have shown stronger links to metabolism. These results demonstrate that the genetic architecture of alcohol consumption only partially overlaps with the genetics of clinically defined AUD. We discuss the limitations of using quantitative measures of alcohol use as proxy measures for AUD, and we outline how future studies will require careful phenotype harmonization to properly capture the genetic liability to AUD.
Topics: Alcohol Dehydrogenase; Alcohol Drinking; Alcoholism; Aldehyde Dehydrogenase, Mitochondrial; Ethanol; Humans; Phenotype; Polymorphism, Single Nucleotide
PubMed: 31733789
DOI: 10.1016/j.biopsych.2019.09.011 -
Angewandte Chemie (International Ed. in... Apr 2021Multienzyme cascade biocatalysis is an efficient synthetic process, avoiding the isolation/purification of intermediates and shifting the reaction equilibrium to the...
Multienzyme cascade biocatalysis is an efficient synthetic process, avoiding the isolation/purification of intermediates and shifting the reaction equilibrium to the product side.. However, multienzyme systems are often limited by their incompatibility and cross-reactivity. Herein, we report a multi-responsive emulsion to proceed multienzyme reactions sequentially for high reactivity. The emulsion is achieved using a CO , pH, and thermo-responsive block copolymer as a stabilizer, allowing the on-demand control of emulsion morphology and phase composition. Applying this system to a three-step cascade reaction enables the individual optimal condition for each enzyme, and a high overall conversion (ca. 97 % of the calculated limit) is thereby obtained. Moreover, the multi-responsiveness of the emulsion allows the facile and separate yielding/recycling of products, polymers and active enzymes. Besides, the system could be scaled up with a good yield.
Topics: Alcohol Dehydrogenase; Aldehyde-Lyases; Biocatalysis; Emulsions; Fungal Proteins; Lipase; Polymers
PubMed: 33480131
DOI: 10.1002/anie.202013737 -
Advances in Experimental Medicine and... 2018Excessive consumption of alcohol is a leading cause of lifestyle-induced morbidity and mortality worldwide. Although long-term alcohol abuse has been shown to be... (Review)
Review
Excessive consumption of alcohol is a leading cause of lifestyle-induced morbidity and mortality worldwide. Although long-term alcohol abuse has been shown to be detrimental to the liver, brain and many other organs, our understanding of the exact molecular mechanisms by which this occurs is still limited. In tissues, ethanol is metabolized to acetaldehyde (mainly by alcohol dehydrogenase and cytochrome p450 2E1) and subsequently to acetic acid by aldehyde dehydrogenases. Intracellular generation of free radicals and depletion of the antioxidant glutathione (GSH) are believed to be key steps involved in the cellular pathogenic events caused by ethanol. With continued excessive alcohol consumption, further tissue damage can result from the production of cellular protein and DNA adducts caused by accumulating ethanol-derived aldehydes. Much of our understanding about the pathophysiological consequences of ethanol metabolism comes from genetically-engineered mouse models of ethanol-induced tissue injury. In this review, we provide an update on the current understanding of important mouse models in which ethanol-metabolizing and GSH-synthesizing enzymes have been manipulated to investigate alcohol-induced disease.
Topics: Acetaldehyde; Alcohol Dehydrogenase; Animals; Cytochrome P-450 CYP2E1; Disease Models, Animal; Ethanol; Mice; Neoplasms
PubMed: 30362100
DOI: 10.1007/978-3-319-98788-0_14 -
Psychological Medicine Oct 2021Substance use disorders (SUDs) are prevalent and result in an array of negative consequences. They are influenced by genetic factors (h2 = ~50%). Recent years have...
Substance use disorders (SUDs) are prevalent and result in an array of negative consequences. They are influenced by genetic factors (h2 = ~50%). Recent years have brought substantial progress in our understanding of the genetic etiology of SUDs and related traits. The present review covers the current state of the field for SUD genetics, including the epidemiology and genetic epidemiology of SUDs, findings from the first-generation of SUD genome-wide association studies (GWAS), cautions about translating GWAS findings to clinical settings, and suggested prioritizations for the next wave of SUD genetics efforts. Recent advances in SUD genetics have been facilitated by the assembly of large GWAS samples, and the development of state-of-the-art methods modeling the aggregate effect of genome-wide variation. These advances have confirmed that SUDs are highly polygenic with many variants across the genome conferring risk, the vast majority of which are of small effect. Downstream analyses have enabled finer resolution of the genetic architecture of SUDs and revealed insights into their genetic relationship with other psychiatric disorders. Recent efforts have also prioritized a closer examination of GWAS findings that have suggested non-uniform genetic influences across measures of substance use (e.g. consumption) and problematic use (e.g. SUD). Additional highlights from recent SUD GWAS include the robust confirmation of loci in alcohol metabolizing genes (e.g. ADH1B and ALDH2) affecting alcohol-related traits, and loci within the CHRNA5-CHRNA3-CHRNB4 gene cluster influencing nicotine-related traits. Similar successes are expected for cannabis, opioid, and cocaine use disorders as sample sizes approach those assembled for alcohol and nicotine.
Topics: Alcohol Dehydrogenase; Alcoholism; Aldehyde Dehydrogenase, Mitochondrial; Cannabis; Gene-Environment Interaction; Genome-Wide Association Study; Humans; Molecular Epidemiology; Nicotine; Substance-Related Disorders
PubMed: 33879270
DOI: 10.1017/S0033291721000969 -
Molecular Psychiatry Aug 2021Alcohol use and smoking are leading causes of death and disability worldwide. Both genetic and environmental factors have been shown to influence individual differences...
Alcohol use and smoking are leading causes of death and disability worldwide. Both genetic and environmental factors have been shown to influence individual differences in the use of these substances. In the present study we tested whether genetic factors, modelled alongside common family environment, explained phenotypic variance in alcohol use and smoking behaviour in the Generation Scotland (GS) family sample of up to 19,377 individuals. SNP and pedigree-associated effects combined explained between 18 and 41% of the variance in substance use. Shared couple effects explained a significant amount of variance across all substance use traits, particularly alcohol intake, for which 38% of the phenotypic variance was explained. We tested whether the within-couple substance use associations were due to assortative mating by testing the association between partner polygenic risk scores in 34,987 couple pairs from the UK Biobank (UKB). No significant association between partner polygenic risk scores were observed. Associations between an individual's alcohol PRS (b = 0.05, S.E. = 0.006, p < 2 × 10) and smoking status PRS (b = 0.05, S.E. = 0.005, p < 2 × 10) were found with their partner's phenotype. In support of this, G carriers of a functional ADH1B polymorphism (rs1229984), known to be associated with greater alcohol intake, were found to consume less alcohol if they had a partner who carried an A allele at this SNP. Together these results show that the shared couple environment contributes significantly to patterns of substance use. It is unclear whether this is due to shared environmental factors, assortative mating, or indirect genetic effects. Future studies would benefit from longitudinal data and larger sample sizes to assess this further.
Topics: Alcohol Dehydrogenase; Alcohol Drinking; Family; Humans; Pedigree; Scotland; Smoking; Tobacco Smoking
PubMed: 31767999
DOI: 10.1038/s41380-019-0607-x