DOCSLIB.ORG

ATP-Binding Site of Adenylate Kinase: Mechanistic Implications of Its Homology with Ras-Encoded P21, Fl-Atpase, and Other Nucleotide-Binding Proteins DAVID C

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
ATP-Binding Site of Adenylate Kinase: Mechanistic Implications of Its Homology with Ras-Encoded P21, Fl-Atpase, and Other Nucleotide-Binding Proteins DAVID C Proc. Natl. Acad. Sci. USA Vol. 83, pp. 907-911, February 1986 Biochemistry ATP-binding site of adenylate kinase: Mechanistic implications of its homology with ras-encoded p21, Fl-ATPase, and other nucleotide-binding proteins DAVID C. FRY*, STEPHEN A. KUBYt, AND ALBERT S. MILDVAN* *Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205; and tLaboratory for the Study of Hereditary and Metabolic Disorders and the Departments of Biological Chemistry and Medicine, University of Utah, Salt Lake City, UT 84108 Communicated by Albert L. Lehninger, October 7, 1985 ABSTRACT The MgATP binding site of adenylate kinase, homologies for which the binding site of the nucleotide located by a combination ofNMR and x-ray diffraction, is near substrate has been characterized. Only one of the three three protein segments, five to seven amino acids in length, that homologous segments is found in phosphofructokinase, for are homologous in sequence to segments found in other which an x-ray structure also exists (14). Such information on nucleotide-binding phosphotransferases, such as myosin and adenylate kinase reveals interactions between the homolo- Fl-ATPase, ras p21 and transducin GTPases, and cAMP- gous residues and the bound nucleotide substrate that permit dependent and src protein kinases, suggesting equivalent reasonable predictions to be made of the functions of such mechanistic roles of these segments in all of these proteins. residues and their near neighbors, not only in adenylate Segment 1 is a glycine-rich flexible loop that, on adenylate kinase but also in the other nucleotide-binding phosphotrans- kinase, may control access to the ATP-binding site by changing ferases, and that rationalize the effects of mutations on both its conformation. Segment 2 is an a-helix containing two the GTPase and transforming activities ofthe ras p21 protein. hydrophobic residues that interact with the adenine-ribose moiety of ATP, and a lysine that may bind to the j8- and Sequence Homologies Among Adenylate Kinase and Other y-phosphates of ATP. Segment 3 is a hydrophobic strand of Proteins parallel a6-pleated sheet, terminated by a carboxylate, that flanks the triphosphate binding site. The various reported mutations of ras p21 that convert it to a transforming agent all In Table 1 portions of the amino acid sequence of rabbit appear to involve segment 1, and such substitutions may alter muscle adenylate kinase are given, and homologous regions the properties of p21 by hindering a conformational change at in the sequences of other proteins are listed. Included are the this segment. In F1-ATPase, the flexible loop may, by its homologies noted by Walker and co-workers (5, 8) and others position, control both the accessibility and the ATP/ADP derived from computer searches and visual inspection of constant on the enzyme. available sequences. There are three segments of homology. equilibrium Clearly, some of the proteins listed in Table 1 show only one or two of the three homologous segments. Segment 1 (resi- Adenylate kinase catalyzes the reversible transfer of a dues 15-21 in adenylate kinase: Gly-Gly-Pro-Gly-Ser-Gly- phosphoryl group from MgATP to AMP. Lys) is shared by several ATPases and GTPases, as well as by DNA A protein, Epstein-Barr virus protein, thymidine MgATP + AMP MgADP + ADP. [1] kinase, cAMP-dependent protein kinase, phospholipase A2, glycogen phosphorylase, nitrogenase, and the biotin-contain- The enzyme has been purified from many sources, the x-ray ing subunit of transcarboxylase.t Slightly further along in the structure of the porcine muscle enzyme has been reported at sequence is segment 2 (residues 27-31: Lys-Ile-Val-His-Lys) 3 A resolution (1), and amino acid sequences have been that bears weak homology to corresponding portions ofmany determined for muscle adenylate kinase from pig (2), human of these proteins and strong homology to regions of the (3), calf, and rabbit (4). It was noted by Walker et al. (5) that protein kinases and transcarboxylase. Segment 3 (residues two portions of the adenylate kinase sequence had homolo- 114-119: Leu-Leu-Leu-Tyr-Val-Asp) has counterparts in the gous counterparts in the sequences of several ATPases. One sequences of F1-ATPase, ras p21, ATP/ADP translocase, of these homologous segments was later found to be present phosphofructokinase, and transcarboxylase. § in p21, the GTPase that is the product of the ras oncogene (6-8). The recent finding that a mutation in this segment is the basis of the transforming ability of this protein (9, 10) has The MgATP Binding Site of Adenylate Kinase amplified the importance ofdetermining the functional role of this segment. We have identified a third homologous region High-field proton NMR was used to study the interaction of in several ofthese proteins and have further expanded the list metal-ATP substrates with porcine (11) and rabbit muscle of proteins with sequence homologies to adenylate kinase. adenylate kinase (12), and with a globular peptide fragment of Through a series of NMR studies on porcine (11) and rabbit the latter enzyme consisting of residues 1-45 that binds muscle (12) adenylate kinase and on an ATP-binding peptide metal-ATP with comparable affinity (13). Paramagnetic ef- fragment of the latter (12, 13), we have located the MgATP fects of B,y-bidentate Cr3+-ATP on the relaxation rates of binding site within the x-ray structure ofthe enzyme and have protons of the enzyme and the peptide were measured and obtained a detailed description of the environment of the provided a total ofeight distances from Cr3+ to the side chains bound nucleotide. Adenylate kinase is the only protein of specific amino acid residues. Time-dependent nuclear among those sharing the aforementioned extensive sequence tIn some of the proteins of Table 1 this homology extends beyond residue 21 to residue 23. The publication costs of this article were defrayed in part by page charge §Regions of near homology to segments 1 and 2 are found in payment. This article must therefore be hereby marked "advertisement" phosphoglycerate kinase (30, 31) and to segment 3 in creatine kinase in accordance with 18 U.S.C. §1734 solely to indicate this fact. (32). 907 Downloaded by guest on September 29, 2021 908 Biochemistry: Fry et al. Proc. Natl. Acad. Sci. USA 83 (1986) Table 1. Sequence homologies among the ATP-binding region of adenylate kinase and segments of other proteins Sequence Protein 15 20 25 30 110 115 120 Adenylate kinasea G-G-P -G-S-G-K-G-T-Q-C-E-K -I-V-H-K G-Q-P-T-L-L-L-Y-V-D-A-G Fl-ATPaseb a(E. coli) G-D-R -Q- -G-K-T- -A-I- G- -A-L-I-I-Y-D-D- f3(E. coli) G-G-A -G- -G-K-T- -L-I- G- -V-L-L-F-V-D- p(bovine) G-G-A -G- -G-K-T- -L-I- G-Q- -V-L-L-F-I-D- Myosinc nematode -G-G -G-G-G-K- -V- G- -G- -G-K-T- -K -V-I- rabbit G- -G- -G-K-T- -R -V-I- Thymidine kinased G- -G- -G-K-T-T- -L-V- RecA protein G- -S-G-K-T-T- -V-I- Transducin ae G- -G- -S-G-K- -T- -K- Go protein ae G- -G- -S-G-K- -T- -K- ras p21f G- -Gg-G- -G-K- -L-I G- -L-L-D-I-L-D-T-Ah DnaA proteini G-G- -G- -G-K-T- -V- Epstein-Barr virus proteins G-G- -G-K-G- -A- Glycogen phosphorylasek G- -G -G- -G-R- -C- Phospholipase A2' G- -G -G- -G-R- Protein kinasem cAMP-dependent G- -G- -G-R- -/10/-Kn-I-L- -K cGMP-dependent -Kn-I-L- -K src protein G- -G- -G- -/10/-Kn-T-L-K- Nitrogenase (Fe protein)0 G- -G -G- -G-K- -T- -/11/-K -I-L- Transcarboxylase biotin subunitP G-G- -G- -G-K- -/10/-K -I-L- -K G-Q-T-V-L-V-L-E -Bct- ATP/ADP translocase G- -V-L-V-L-Y-D Phosphofructokinase G- -L-V-V-I- -D- aThe sequence of rabbit muscle adenylate kinase is from Kuby et al. (4). bComparisons involving Fl-ATPases, myosin, RecA protein, translocase, and phosphofructokinase are from Walker et al. (5). cThe upper homologous sequence of nematode myosin is an alternative region to that (lower) presented by Walker et al. (5). dSequence of the thymidine kinase from herpes simplex virus is from McKnight (15). ePartial sequences of the subunits of transducin from bovine retina and G. protein from bovine brain are from Hurley et al. (16). 'the sequence of a ras gene product is typified by that from the c-has/bas human protooncogene (17). Some homology involving this protein has been noted by Gay and Walker (8). gMutations at this position alter the transforming ability (9, 10, 18-21) and GTPase activity (18-20) of the protein. hSubstitution of a threonine at this position apparently results in autophosphorvlation (18). Sequence from Hansen et al. (22). Sequence from Bankier et al. (23). kSequence from Titani et al. (24). 'Sequence from Joubert and Haylett (25). mATP-binding site sequence for cAMP-dependent protein kinase, and partial sequence for cGMP-dependent protein kinase, were obtained from Hashimoto et al. (26). Comparison between these sequences and that of p6osrc, the transforming tyrosine kinase of Rous sarcoma virus, is from Kamps et al. (27). nThis lysine is the residue labeled during inactivation with p-fluorosulfonylbenzoyl 5'-adenosine (27). °Sequence of the Fe-protein of nitrogenase and some of the homology involving this protein is from Robson (28).
Load more

Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
    [Show full text]
  • Allosteric Regulation in Drug Design
    Mini Review Curr Trends Biomedical Eng & Biosci Volume 4 Issue 1 - May 2017 Copyright © All rights are reserved by Ashfaq Ur Rehman DOI: 10.19080/CTBEB.2017.04.5555630 Allosteric regulation in drug design Ashfaq Ur Rehman1,2*, Shah Saud3, Nasir Ahmad4, Abdul Wadood2 and R Hamid5 1State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, China 2Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan 3Laboratory of Analytical Biochemistry and Bio separation, Shanghai Jiao Tong University, China 4Department of Chemistry, Islama College University Peshawar, Pakistan 5Department of Bioinformatics, Muhammad Ali Jinnah University Islamabad, Pakistan Submission: May 02, 2017; Published: May 23, 2017 *Corresponding author: Ashfaq Ur Rehman, State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China, Tel: ; Fax: 86-21-34204348; Email: Abstract mechanism, which are initiated through attachment of ligand or inhibitors with the protein or enzymes other than active (orthosteric) sites. ThisProtein mini review and enzymes involved play mechanism, significant types roles and in importancebiological processes of allosteric of all regulations living organisms; in drug theirdesign functions process. are regulated through allosteric Keywords: Allosteric, Activator: Drug design Introduction and ultimately cause disease. While various biological processes expressed the control at different points in life time of protein function is pivotal. As all the cell processes are under carful For the survival of all organisms the significance of protein included regulation of gene expression, translation into protein control and if not properly controls this leads to the abnormality through control of activity and at last degradation of protein [1].
    [Show full text]
  • Tyrosine Kinase – Role and Significance in Cancer
    Int. J. Med. Sci. 2004 1(2): 101-115 101 International Journal of Medical Sciences ISSN 1449-1907 www.medsci.org 2004 1(2):101-115 ©2004 Ivyspring International Publisher. All rights reserved Review Tyrosine kinase – Role and significance in Cancer Received: 2004.3.30 Accepted: 2004.5.15 Manash K. Paul and Anup K. Mukhopadhyay Published:2004.6.01 Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S Nagar, Mohali, Punjab, India-160062 Abstract Tyrosine kinases are important mediators of the signaling cascade, determining key roles in diverse biological processes like growth, differentiation, metabolism and apoptosis in response to external and internal stimuli. Recent advances have implicated the role of tyrosine kinases in the pathophysiology of cancer. Though their activity is tightly regulated in normal cells, they may acquire transforming functions due to mutation(s), overexpression and autocrine paracrine stimulation, leading to malignancy. Constitutive oncogenic activation in cancer cells can be blocked by selective tyrosine kinase inhibitors and thus considered as a promising approach for innovative genome based therapeutics. The modes of oncogenic activation and the different approaches for tyrosine kinase inhibition, like small molecule inhibitors, monoclonal antibodies, heat shock proteins, immunoconjugates, antisense and peptide drugs are reviewed in light of the important molecules. As angiogenesis is a major event in cancer growth and proliferation, tyrosine kinase inhibitors as a target for anti-angiogenesis can be aptly applied as a new mode of cancer therapy. The review concludes with a discussion on the application of modern techniques and knowledge of the kinome as means to gear up the tyrosine kinase drug discovery process.
    [Show full text]
  • DNA Breakpoint Assay Reveals a Majority of Gross Duplications Occur in Tandem Reducing VUS Classifications in Breast Cancer Predisposition Genes
    © American College of Medical Genetics and Genomics ARTICLE Corrected: Correction DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes Marcy E. Richardson, PhD1, Hansook Chong, PhD1, Wenbo Mu, MS1, Blair R. Conner, MS1, Vickie Hsuan, MS1, Sara Willett, MS1, Stephanie Lam, MS1, Pei Tsai, CGMBS, MB (ASCP)1, Tina Pesaran, MS, CGC1, Adam C. Chamberlin, PhD1, Min-Sun Park, PhD1, Phillip Gray, PhD1, Rachid Karam, MD, PhD1 and Aaron Elliott, PhD1 Purpose: Gross duplications are ambiguous in terms of clinical cohort, while the remainder have unknown tandem status. Among interpretation due to the limitations of the detection methods that the tandem gross duplications that were eligible for reclassification, cannot infer their context, namely, whether they occur in tandem or 95% of them were upgraded to pathogenic. are duplicated and inserted elsewhere in the genome. We Conclusion: DBA is a novel, high-throughput, NGS-based method investigated the proportion of gross duplications occurring in that informs the tandem status, and thereby the classification of, tandem in breast cancer predisposition genes with the intent of gross duplications. This method revealed that most gross duplica- informing their classifications. tions in the investigated genes occurred in tandem and resulted in a Methods: The DNA breakpoint assay (DBA) is a custom, paired- pathogenic classification, which helps to secure the necessary end, next-generation sequencing (NGS) method designed to treatment options for their carriers. capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2. Genetics in Medicine (2019) 21:683–693; https://doi.org/10.1038/s41436- Results: DBA allowed us to ascertain breakpoints for 44 unique 018-0092-7 gross duplications from 147 probands.
    [Show full text]
  • In the Field of Clinical Examination, the Measurement of Creatine
    J. Clin. Biochem. Nutr., 3, 17-25, 1987 Bacterial Glucokinase as an Enzymic Reagent of Good Stability for Measurement of Creatine Kinase Activity Hitoshi KONDO, * Takanari SHIRAISHI, Masao KAGEYAMA, Kazuhiko NAGATA, and Kosuke TOMITA Research and Development Center, UNITIKA Ltd., Uji 611, Japan (Received January 10, 1987) Summary An enzymic reagent, that has long-term stability even in the liquid state, was successfully employed for the measurement of serum creatine kinase (CK, EC 2.7.3.2) activity. The enzyme used was the thermostable glucokinase (GlcK, EC 2.7.1.2) obtained from the thermo- phile Bacillus stearothermophilus. The reagent was found to be stable in solution for about one month at 6•Ž and for about one week at 30•Ž. This substitution of glucokinase for the hexokinase of the most commonly used hexokinase-glucose-6-phosphate dehydrogenase (HK-G6PDH) method results in a remarkable improvement of the method. The CK activity measured by the GlcK-G6PDH method was linear up to about 2,000 U/ liter at 37•Ž. The GlcK-G6PDH method was found to give a satisfactory precision and reproducibility (coefficient of variation less than 2.17%). Over a wide range of CK activity, an excellent agreement was obtained between the GlcK-G6PDH and the HK-G6PDH methods. Furthermore several coexistents and anticoagulants were found to have little effect on the measured value of CK activity by the GlcK-G6PDH method. Key Words: creatine kinase activity, glucokinase, improved stability of reagent, creatine kinase determination, thermostable enzyme In the field of clinical examination, the measurement of creatine kinase (CK, ATP : creatine phosphotransferase, EC 2.7.3.2) activity in serum is one of the important examinations usually employed for diagnosis of cardiac diseases such as myocardial infarction or muscular diseases such as progressive muscular dystrophy.
    [Show full text]
  • Labeled in Thecourse of Glycolysis, Since Phosphoglycerate Kinase
    THE STATE OF MAGNESIUM IN CELLS AS ESTIMATED FROM THE ADENYLATE KINASE EQUILIBRIUM* BY TRWIN A. RoSE THE INSTITUTE FOR CANCER RESEARCH, PHILADELPHIA Communicated by Thomas F. Anderson, August 30, 1968 Magnesium functions in many enzymatic reactions as a cofactor and in com- plex with nucleotides acting as substrates. Numerous examples of a possible regulatory role of Mg can be cited from studies with isolated enzymes,'- and it is known that Mg affects the structural integrity of macromolecules such as trans- fer RNA" and functional elements such as ribosomes.'0 The major problem in translating this information on isolated preparations to the functioning cell is the difficulty in determining the distribution of Mg and the nucleotides among the free and complexed forms that function in the region of the cell for which this information is desired. Nanningall based an attempt to calculate the free Mg2+ and Ca2+ ion concentrations of frog muscle on the total content of these metals and of the principal known ligands (adenosine 5'-triphosphate (ATP), creatine-P, and myosin) and the dissociation constants of the complexes. However, this method suffers from the necessity of evaluating the contribution of all ligands as well as from the assumption that all the known ligands are contributing their full complexing capacity. During studies concerned with the control of glycolysis in red cells and the control of the phosphoglycerate kinase step in particular, it became important to determine the fractions of the cell's ATP and adenosine 5'-diphosphate (ADP) that were present as Mg complexes. Just as the problem of determining the distribution of protonated and dissociated forms of an acid can be solved from a knowledge of pH and pKa of the acid, so it would be possible to determine the liganded and free forms of all rapidly established Mg complexes from a knowledge of Mg2+ ion concentration and the appropriate dissociation constants.
    [Show full text]
  • Integrated Computational Approaches and Tools for Allosteric Drug Discovery
    International Journal of Molecular Sciences Review Integrated Computational Approaches and Tools for Allosteric Drug Discovery Olivier Sheik Amamuddy 1 , Wayde Veldman 1 , Colleen Manyumwa 1 , Afrah Khairallah 1 , Steve Agajanian 2, Odeyemi Oluyemi 2, Gennady M. Verkhivker 2,3,* and Özlem Tastan Bishop 1,* 1 Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; [email protected] (O.S.A.); [email protected] (W.V.); [email protected] (C.M.); [email protected] (A.K.) 2 Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; [email protected] (S.A.); [email protected] (O.O.) 3 Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA * Correspondence: [email protected] (G.M.V.); [email protected] (Ö.T.B.); Tel.: +714-516-4586 (G.M.V.); +27-46-603-8072 (Ö.T.B.) Received: 25 December 2019; Accepted: 21 January 2020; Published: 28 January 2020 Abstract: Understanding molecular mechanisms underlying the complexity of allosteric regulation in proteins has attracted considerable attention in drug discovery due to the benefits and versatility of allosteric modulators in providing desirable selectivity against protein targets while minimizing toxicity and other side effects. The proliferation of novel computational approaches for predicting ligand–protein interactions and binding using dynamic and network-centric perspectives has led to new insights into allosteric mechanisms and facilitated computer-based discovery of allosteric drugs. Although no absolute method of experimental and in silico allosteric drug/site discovery exists, current methods are still being improved.
    [Show full text]
  • The Characterization of Human Adenylate Kinases 7 and 8
    The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes Christakis Panayiotou, Nicola Solaroli, Yunjian Xu, Magnus Johansson, Anna Karlsson To cite this version: Christakis Panayiotou, Nicola Solaroli, Yunjian Xu, Magnus Johansson, Anna Karlsson. The char- acterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes. Biochemical Journal, Port- land Press, 2011, 433 (3), pp.527-534. 10.1042/BJ20101443. hal-00558097 HAL Id: hal-00558097 https://hal.archives-ouvertes.fr/hal-00558097 Submitted on 21 Jan 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Biochemical Journal Immediate Publication. Published on 16 Nov 2010 as manuscript BJ20101443 The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes
    [Show full text]
  • Tyrosine Kinases
    KEVANM SHOKAT MINIREVIEW Tyrosine kinases: modular signaling enzymes with tunable specificities Cytoplasmic tyrosine kinases are composed of modular domains; one (SHl) has catalytic activity, the other two (SH2 and SH3) do not. Kinase specificity is largely determined by the binding preferences of the SH2 domain. Attaching the SHl domain to a new SH2 domain, via protein-protein association or mutation, can thus dramatically change kinase function. Chemistry & Biology August 1995, 2:509-514 Protein kinases are one of the largest protein families identified, This is a result of the overlapping substrate identified to date; over 45 new members are identified specificities of many tyrosine kinases, which makes it each year. It is estimated that up to 4 % of vertebrate pro- difficult to dissect the individual signaling pathways by teins are protein kinases [l].The protein kinases are cate- scanning for unique target motifs [2]. gorized by their specificity for serineithreonine, tyrosine, or histidine residues. Protein tyrosine kinases account for The apparent promiscuity of individual tyrosine kinases roughly half of all kinases. They occur as membrane- is a result of their unique structural organization. bound receptors or cytoplasmic proteins and are involved Enzyme specificity is typically programmed by one in a wide variety of cellular functions, including cytokine binding site, which recognizes the substrate and also con- responses, antigen-dependent immune responses, cellular tains exquisitely oriented active-site functional groups transformation by RNA viruses, oncogenesis, regulation that help to lower the energy of the transition state for of the cell cycle, and modification of cell morphology the conversion of specific substrates to products.Tyrosine (Fig.
    [Show full text]
  • Structure and Evolution of Protein Allosteric Sites
    Structure and evolution of protein allosteric sites by Alejandro Panjkovich Thesis submitted to Universitat Aut`onoma de Barcelona in partial fulfillment of the requirements for the degree of Doctor of Philosophy Director - Prof. Xavier Daura Tesi Doctoral UAB/ANY 2013 Ph.D. Program - Protein Structure and Function Institut de Biotecnologia i Biomedicina caminante, no hay camino, se hace camino al andar Antonio Machado,1912 Acknowledgements First of all I would like to thank my supervisor and mentor Prof. Xavier Daura for his consistent support and trust in my work throughout these years. Xavi, I deeply appreciate the freedom you gave me to develop this project while you were still carefully aware of the small details. Working under your supervision has been a rich and fulfilling experience. Of course, thanks go as well to current and past members of our institute, especially Rita Rocha, Pau Marc Mu˜noz,Oscar Conchillo, Dr. Mart´ınIndarte, Dr. Mario Ferrer, Prof. Isidre Gibert, Dr. Roman Affentranger and Dr. Juan Cedano for their technical and sometimes philo- sophical assistance. Help from the administrative staff was also significant, I would like to thank in particular Eva, Alicia and Miguel who where always ready to help me in sorting out unexpected bureaucratic affairs. I would also like to thank Dr. Mallur Srivatasan Madhusudhan and his group (especially Kuan Pern Tan, Dr. Minh Nguyen and Binh Nguyen), and also Dr. Gloria Fuentes, Cassio Fernandes, Youssef Zaki, Thijs Kooi, Rama Iyer, Christine Low and many others at the Bioinformatics Institute BII - A∗STAR in Singapore for the many interesting discussions and support during my stage over there.
    [Show full text]
  • Understanding Drug-Drug Interactions Due to Mechanism-Based Inhibition in Clinical Practice
    pharmaceutics Review Mechanisms of CYP450 Inhibition: Understanding Drug-Drug Interactions Due to Mechanism-Based Inhibition in Clinical Practice Malavika Deodhar 1, Sweilem B Al Rihani 1 , Meghan J. Arwood 1, Lucy Darakjian 1, Pamela Dow 1 , Jacques Turgeon 1,2 and Veronique Michaud 1,2,* 1 Tabula Rasa HealthCare Precision Pharmacotherapy Research and Development Institute, Orlando, FL 32827, USA; [email protected] (M.D.); [email protected] (S.B.A.R.); [email protected] (M.J.A.); [email protected] (L.D.); [email protected] (P.D.); [email protected] (J.T.) 2 Faculty of Pharmacy, Université de Montréal, Montreal, QC H3C 3J7, Canada * Correspondence: [email protected]; Tel.: +1-856-938-8697 Received: 5 August 2020; Accepted: 31 August 2020; Published: 4 September 2020 Abstract: In an ageing society, polypharmacy has become a major public health and economic issue. Overuse of medications, especially in patients with chronic diseases, carries major health risks. One common consequence of polypharmacy is the increased emergence of adverse drug events, mainly from drug–drug interactions. The majority of currently available drugs are metabolized by CYP450 enzymes. Interactions due to shared CYP450-mediated metabolic pathways for two or more drugs are frequent, especially through reversible or irreversible CYP450 inhibition. The magnitude of these interactions depends on several factors, including varying affinity and concentration of substrates, time delay between the administration of the drugs, and mechanisms of CYP450 inhibition. Various types of CYP450 inhibition (competitive, non-competitive, mechanism-based) have been observed clinically, and interactions of these types require a distinct clinical management strategy. This review focuses on mechanism-based inhibition, which occurs when a substrate forms a reactive intermediate, creating a stable enzyme–intermediate complex that irreversibly reduces enzyme activity.
    [Show full text]
  • Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
    Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6
    [Show full text]