DOCSLIB.ORG

Insights Into Enzyme Allosteric Inhibition Mechanisms Using Computational Studies

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Insights Into Enzyme Allosteric Inhibition Mechanisms Using Computational Studies Insights into enzyme allosteric inhibition mechanisms using computational studies A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry at the University of Canterbury by Eric Jean Maurice Lang April 2016 Abstract Allostery, the process by which action of an effector at one site of the protein provokes a functional response at a distant site, is critical in the regulation of metabolic pathways. Yet, despite its importance, allostery remains enigmatic and little detailed information is known about how the function of the protein is affected, how the allosteric signal is communicated or how allosteric regulation evolves in a protein. The overall objective of this thesis is to provide new insights into the understanding of allostery by studying computationally allosteric regulation in the metabolic enzyme 3-deoxy- D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) which catalyses the first committed step in the biosynthesis of aromatic amino acids. Not only is DAH7PS a promising antimicrobial drug target, owing to its presence in microorganisms but not in animals, but also, the unique variety of allosteric regulation mechanisms found in this protein family makes it the ideal playground to study allostery. Firstly, in Chapter 2, using a variety of sequence and phylogenetic analysis tools, the evolution of allosteric regulation in the DAH7PS family was explored. New subgroups of the DAH7PS family were identified and it was found that DAH7PS is likely to have acquired allostery by the recruitment of an N- or C-terminal regulatory domain via gene fusion. Loop i extensions and N-terminal domain mutations then gave rise to more complex allosteric regulation mechanisms. In Chapter 3, a new computational method, which is based on the monitoring of calculated pKa variations of ionisable residues over the course of molecular dynamics simulations, is used to identify allosteric communication pathways in protein relying on dynamic allosteric regulation. This approach is used to decipher the subtle allosteric regulation mechanism of DAH7PS from pathogen Neisseria meningitidis. A number of key charge-charge and hydrogen bond interactions were identified as being responsible for the communication of the allosteric signal in this protein. These predictions were verified experimentally and showed that pH variations can mimic the allosteric control, by changing the protonation state of the residues involved in the identified key interactions. The allosteric regulation of the DAH7PS from hyperthermophile Thermotoga maritima, which relies on major domain motions, is explored using molecular dynamics simulations in Chapter 4. It was found that the flexibility of the allosteric domains impedes the entrance to the active site, explaining the lower catalytic activity observed experimentally when compared to a mutant lacking the regulatory domains. Furthermore, the simulations revealed that although the inhibition of the enzyme is achieved by blocking the access to the active site, the residual activity of the enzyme at high inhibitor concentrations observed experimentally, can be explained by the opening of a back door providing direct access to the catalytic site. In Chapter 5, using a combination of X-ray crystallography, homology modelling and small-angle X-ray scattering, the allosteric regulation mechanism of DAH7PS from thermophilic soil bacterium Geobacillus sp. was studied. These methods revealed that binding ii of the allosteric ligand to the allosteric regulatory domains stabilises a more compact conformation of the protein, limiting the catalytic functionality of the DAH7PS domain active site. In addition, molecular dynamics simulations are currently in progress to further explore the allosteric regulation of this enzyme are presented. In Chapter 6, the different attempts to model the first step of the reaction catalysed by DAH7PS, using hybrid quantum mechanics / molecular mechanics simulations, are presented and recommendations for future work toward the complete modelling of the reaction are provided. Finally, the implications of this work are discussed in the general context of allosteric regulation mechanisms. iii iv Deputy Vice-Chancellor’s Office Postgraduate Office Co-Authorship Form This form is to accompany the submission of any thesis that contains research reported in co-authored work that has been published, accepted for publication, or submitted for publication. A copy of this form should be included for each co-authored work that is included in the thesis. Completed forms should be included at the front (after the thesis abstract) of each copy of the thesis submitted for examination and library deposit. Please indicate the chapter/section/pages of this thesis that are extracted from co-authored work and provide details of the publication or submission from the extract comes: Chapter 3 Lang EJM, Heyes LC, Jameson GB, Parker EJ: Calculated pKa Variations Expose Dynamic Allosteric Communication Networks. Journal of the American Chemical Society 2016, 138:2036-2045 Please detail the nature and extent (%) of contribution by the candidate: 65% Eric Lang designed the key methodlology and carried out the research. He wrote the majority of the manuscript, which was edited and contributed to by co-authors. Certification By Co-authors: If there is more than one co-author then a single co-author can sign on behalf of all The undersigned certifys that: The above statement correctly reflects the nature and extent of the PhD candidate’s contribution to this co-authored work In cases where the candidate was the lead author of the co-authored work he or she wrote the text Name: Emily Parker Signature: Date: 6 April 2016 vi Acknowledgements First and foremost, I would like to express my most sincere gratitude to Professor Emily Parker for giving me this fantastic opportunity but also for being the most amazing supervisor I could have hoped for, leaving me the freedom to explore the areas I was interested in, providing me support, guidance and recommendations, making sure I had access to enough computational resources, facilitating collaborations and helping me to grow as a researcher. Thank you so much for everything Emily. I am very grateful to Professor Adrian Mulholland, for hosting me for a month so I could gain hands-on experience in QM/MM modelling and for enabling me to access Bristol University supercomputer. Considerable thanks must go to Dr Marc Van der Kamp, who provided me with invaluable training in QM/MM modelling and shared his extensive experience with me while helping me running my own QM/MM calculations. Thank you to Associate Professor Anthony Poole for guiding me through the abundance of bioinformatics tools and the diversity of practices that would have, otherwise, been daunting, and for providing me with critical recommendations on the analysis of my bioinformatics results. vii Thank you to Dr Wanting Jiao for helping me with my first molecular dynamics (MD) simulations and providing me with useful recommendations, but also for rapidly leaving me to work on my own so I could gain confidence in running MD simulations and develop my own critical appraisal of the different MD techniques. One of the aspect I enjoyed the most while working in the Parker group was the opportunity I had to collaborate and exchange ideas with experimental chemists and biochemists. Thanks to Dr Logan Heyes, for our fruitful collaboration on NmeDAH7PS and our extensive conversations on the interpretation of our results. Thanks to Yifei Fan for involving me in the preparation of the FRET experiments for GspDAH7PS and TmaDAH7PS, but also for our enjoyable chats about everything. Thanks to Yu Bai, for our collaboration on the SAXS analysis of GspDAH7PS and for our interesting discussions on so many subjects. Thanks to Thomas Cotton for explaining me some of the techniques used in the lab and for our entertaining exchanges. Thanks to Gert-Jan Moggre, for our interesting talks on QM modelling. Thanks to Jordyn Moore for the work on TmaDAH7PS. Thanks to Dr Penel Cross for useful discussions on TmaDAH7PS and on the analysis of SAXS experiments for GspDAH7PS. Thanks also to all the other past and present members of the Parker group, in particular, Dr Nicola Blackmore and Dr Leyla Bustamante for your support, but also Dr Ali Reza Nazmi, Dr Dmitri Joseph, Dr Tammie Cookson, and Sarah Wilson-Coutts. Thank you to Professor Geoffrey Jameson for your wisdom, keen attention to details and critical comments during the writing of the two articles we co-authored. I am grateful to Dr Benjamin Roberts for the very useful recommendations on the minimisation, heating and equilibration protocols and on periodic images. I thank Dr Deborah Crittenden for her remarks and input. Thank you to Dr Jane Allison for our useful discussions. viii I would like to thank the University of Canterbury High-Performance Computing (UCHPC) and New Zealand eScience Infrastructure (NeSI) teams for their support and for ensuring that everything ran smoothly. I thank in particular Dr François Bissey, Gene Soudlenkov, Dan Sun, Peter Maxwell, Jordi Blasco, Dr Celine Cattoen-Gilbert, Charles Bacon and Tony Dale. Thank you to Dr Sung Bae for writing the script that enables to restart automatically the MD simulations on UCHPC systems, and for helping me with the python scripts for the pKa analysis. I thank UCHPC for providing me with a doctoral scholarship to undertake my research as well as for the unlimited amount of core hours on UCHPC systems and for the travel fund. I also thank the Biomolecular Interaction Centre for providing me with a research scholarship for the last six months of my thesis and NeSI for allocating me more than 100,000 CPU/hours on the University of Auckland supercomputer. Thank you to my family and my family-in-law for their support and encouragement from overseas via email and Skype. Finally, to Sybile, thank you so much for having accepted to move to the other side of the world so I could live my dreams, for your constant support, for your encouragements, for believing in me, for your love, for our daughter.
Load more

Recommended publications
  • Adaptive Responses by Transcriptional Regulators to Small Molecules in Prokaryotes
    Adaptive Responses by Transcriptional Regulators to small molecules in Prokaryotes Structural studies of two bacterial one-component signal transduction systems DntR and HpNikR Cyril Dian Stockholm University Doctoral thesis © Cyril Dian, Stockholm 2007 ISBN 978-91-7155-500-7 Department of Biochemistry and Biophysics The Arrhenius Laboratories for Natural Sciences Stockholm University SE-106 91 Stockholm Sweden All previously published papers are reprinted With permission from the publishers Intellecta Docusys, Stockholm 2007 Abstract Prokaryotes are continually exposed to environmental changes in their physiological conditions. In order to survive such unstable conditions, or to compete with others species for the same environmental niche, prokaryotes must monitor signals about both their extracellular environment and intracellular physiological status and provide rapid and appropriate responses to variations in their surroundings. This adaptive response to environmental signals is triggered mainly by transcriptional regulators via two components, the one- and two-component signal transduction systems. These scan intra- and extracellular small-molecule mixtures and modulate gene expression to provide the appropriate physiological response to the prevailing conditions. Most prokaryotic one component regulators are simple transcription factors comprising of a small-molecule binding domain (SMBD) and a DNA binding domain (DBD). Although the effects of transcription factors on the transcription machinery are well understood, the exact location
    [Show full text]
  • Regulation of Stringent Factor by Branched-Chain Amino Acids
    Regulation of stringent factor by branched-chain amino acids Mingxu Fanga and Carl E. Bauera,1 aMolecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405 Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved May 9, 2018 (received for review February 21, 2018) When faced with amino acid starvation, prokaryotic cells induce a Under normal growth conditions, the synthetase activity of Rel is stringent response that modulates their physiology. The stringent thought to be self-inhibited; however, during times of amino acid response is manifested by production of signaling molecules starvation, Rel interacts with stalled ribosomes, which activates guanosine 5′-diphosphate,3′-diphosphate (ppGpp) and guanosine synthetase activity to produce (p)ppGpp. The regulation of hy- 5′-triphosphate,3′-diphosphate (pppGpp) that are also called drolase activity is less understood but may involve one or more alarmones. In many species, alarmone levels are regulated by a downstream domains called the TGS and ACT domains. The TGS multidomain bifunctional alarmone synthetase/hydrolase called domain of SpoT has been shown to interact with an acyl carrier Rel. In this enzyme, there is an ACT domain at the carboxyl region protein, so it is presumed to sense the status of fatty acid metab- that has an unknown function; however, similar ACT domains are olism in E. coli (4). The function of the ACT domain is not as clear; present in other enzymes that have roles in controlling amino acid however, recent cryo-EM structures of E. coli RelA show that this metabolism. In many cases, these other ACT domains have been domain is involved in binding deacyl-tRNA as well as the ribosome shown to allosterically regulate enzyme activity through the bind- (5–7).
    [Show full text]
  • Protein Interactions with the Glucose Transporter Binding Protein GLUT1CBP That Provide a Link Between GLUT1 and the Cytoskeleton Robert C
    Molecular Biology of the Cell Vol. 10, 819–832, April 1999 Protein Interactions with the Glucose Transporter Binding Protein GLUT1CBP That Provide a Link between GLUT1 and the Cytoskeleton Robert C. Bunn, Mari Anne Jensen, and Brent C. Reed* The Department of Biochemistry and Molecular Biology, Louisiana State University School of Medicine, Shreveport, Louisiana 71130-3932 Submitted October 27, 1998; Accepted January 19, 1999 Monitoring Editor: Guido Guidotti Subcellular targeting and the activity of facilitative glucose transporters are likely to be regulated by interactions with cellular proteins. This report describes the identification and characterization of a protein, GLUT1 C-terminal binding protein (GLUT1CBP), that binds via a PDZ domain to the C terminus of GLUT1. The interaction requires the C-terminal four amino acids of GLUT1 and is isoform specific because GLUT1CBP does not interact with the C terminus of GLUT3 or GLUT4. Most rat tissues examined contain both GLUT1CBP and GLUT1 mRNA, whereas only small intestine lacked detectable GLUT1CBP protein. GLUT1CBP is also expressed in primary cultures of neurons and astrocytes, as well as in Chinese hamster ovary, 3T3-L1, Madin–Darby canine kidney, Caco-2, and pheochromocytoma-12 cell lines. GLUT1CBP is able to bind to native GLUT1 extracted from cell membranes, self-associate, or interact with the cytoskeletal proteins myosin VI, a-actinin-1, and the kinesin superfamily protein KIF-1B. The presence of a PDZ domain places GLUT1CBP among a growing family of structural and regulatory proteins, many of which are localized to areas of membrane specialization. This and its ability to interact with GLUT1 and cytoskeletal proteins implicate GLUT1CBP in cellular mechanisms for targeting GLUT1 to specific subcellular sites either by tethering the transporter to cytoskeletal motor proteins or by anchoring the transporter to the actin cytoskeleton.
    [Show full text]
  • Regulation of Stringent Factor by Branched-Chain Amino Acids
    Regulation of stringent factor by branched-chain amino acids Mingxu Fanga and Carl E. Bauera,1 aMolecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405 Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved May 9, 2018 (received for review February 21, 2018) When faced with amino acid starvation, prokaryotic cells induce a Under normal growth conditions, the synthetase activity of Rel is stringent response that modulates their physiology. The stringent thought to be self-inhibited; however, during times of amino acid response is manifested by production of signaling molecules starvation, Rel interacts with stalled ribosomes, which activates guanosine 5′-diphosphate,3′-diphosphate (ppGpp) and guanosine synthetase activity to produce (p)ppGpp. The regulation of hy- 5′-triphosphate,3′-diphosphate (pppGpp) that are also called drolase activity is less understood but may involve one or more alarmones. In many species, alarmone levels are regulated by a downstream domains called the TGS and ACT domains. The TGS multidomain bifunctional alarmone synthetase/hydrolase called domain of SpoT has been shown to interact with an acyl carrier Rel. In this enzyme, there is an ACT domain at the carboxyl region protein, so it is presumed to sense the status of fatty acid metab- that has an unknown function; however, similar ACT domains are olism in E. coli (4). The function of the ACT domain is not as clear; present in other enzymes that have roles in controlling amino acid however, recent cryo-EM structures of E. coli RelA show that this metabolism. In many cases, these other ACT domains have been domain is involved in binding deacyl-tRNA as well as the ribosome shown to allosterically regulate enzyme activity through the bind- (5–7).
    [Show full text]
  • Diana Manuela Pinto Barros Classification and Structure-Based Inference of Transcriptional Regulatory Proteins
    Universidade do Minho Departamento de Informatica´ Diana Manuela Pinto Barros Classification and Structure-Based Inference of Transcriptional Regulatory Proteins June, 2016 Universidade do Minho Departamento de Informatica´ Diana Manuela Pinto Barros Classification and Structure-Based Inference of Transcriptional Regulatory Proteins Tese de Mestrado Mestrado em Bioinformatica´ Trabalho efetuado sobre a orientac¸ao˜ de Sonia´ Carneiro Analia´ Lourenc¸o June, 2016 Acknowledgements I’d like to thank my advisors, Sonia´ Carneiro, for all of the essential input, guidance and time she has conceded this work, otherwise impossible to develop and Analia´ Lourenc¸o, for her valuable time and advices throughout this journey. I want to give the biggest thanks to my family. To my parents, Fernando and Inesˆ Barros for always believing in me and for giving me opportunities that weren’t given to them. Thank you for not giving up on me and for making me the person I am today. To my brothers, Sergio´ e Pedro. You are examples of perseverance and success that I can only hope to achieve one day. To my grandparents, Maria da Conceic¸ao˜ Silva e Antonio´ Ferreira Pinto for being the type of people I want to become some day and for being an example that I could always look up to. To my aunts: Em´ılia Pinto and Luz Pinto, my extra mothers, for being light in times of need and providing me the hope and strength when I had none left. I wouldn’t have made it this far without you. I want to thank all my friends that have accompanied me throughout this adventure.
    [Show full text]
  • The C-Di-AMP Receptor Darb Controls (P)Ppgpp Synthesis in Bacillus Subtilis
    ARTICLE https://doi.org/10.1038/s41467-021-21306-0 OPEN A meet-up of two second messengers: the c-di-AMP receptor DarB controls (p)ppGpp synthesis in Bacillus subtilis Larissa Krüger1, Christina Herzberg1, Dennis Wicke1, Heike Bähre2, Jana L. Heidemann3, Achim Dickmanns3, ✉ Kerstin Schmitt4, Ralf Ficner 3 & Jörg Stülke 1 1234567890():,; Many bacteria use cyclic di-AMP as a second messenger to control potassium and osmotic homeostasis. In Bacillus subtilis, several c-di-AMP binding proteins and RNA molecules have been identified. Most of these targets play a role in controlling potassium uptake and export. In addition, c-di-AMP binds to two conserved target proteins of unknown function, DarA and DarB, that exclusively consist of the c-di-AMP binding domain. Here, we investigate the function of the c-di-AMP-binding protein DarB in B. subtilis, which consists of two cystathionine-beta synthase (CBS) domains. We use an unbiased search for DarB interaction partners and identify the (p)ppGpp synthetase/hydrolase Rel as a major interaction partner of DarB. (p)ppGpp is another second messenger that is formed upon amino acid starvation and under other stress conditions to stop translation and active metabolism. The interaction between DarB and Rel only takes place if the bacteria grow at very low potassium con- centrations and intracellular levels of c-di-AMP are low. We show that c-di-AMP inhibits the binding of DarB to Rel and the DarB–Rel interaction results in the Rel-dependent accumu- lation of pppGpp. These results link potassium and c-di-AMP signaling to the stringent response and thus to the global control of cellular physiology.
    [Show full text]
  • Serine Dehydratase from Legionella Pneumophila: Novel Use of the C‑Terminal Cysteine As an Intrinsic Competitive Inhibitor † † ‡ James B
    Article pubs.acs.org/biochemistry Structure of L‑Serine Dehydratase from Legionella pneumophila: Novel Use of the C‑Terminal Cysteine as an Intrinsic Competitive Inhibitor † † ‡ James B. Thoden, Hazel M. Holden,*, and Gregory A. Grant*, † Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States ‡ Department of Developmental Biology and Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States ABSTRACT: Here we report the first complete structure of a bacterial Fe−S L- serine dehydratase determined to 2.25 Å resolution. The structure is of the type 2 L- serine dehydratase from Legionella pneumophila that consists of a single polypeptide chain containing a catalytic α domain and a β domain that is structurally homologous to the “allosteric substrate binding” or ASB domain of D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis. The enzyme exists as a dimer of identical subunits, with each subunit exhibiting a bilobal architecture. The [4Fe-4S]2+ cluster is bound by residues from the C-terminal α domain and is situated between this domain and the N-terminal β domain. Remarkably, the model reveals that the C- terminal cysteine residue (Cys 458), which is conserved among the type 2 L-serine dehydratases, functions as a fourth ligand to the iron−sulfur cluster producing a “tail in mouth” configuration. The interaction of the sulfhydryl group of Cys 458 with the fourth iron of the cluster appears to mimic the position that the substrate would adopt prior to catalysis. A number of highly conserved or invariant residues found in the β domain are clustered around the iron−sulfur center.
    [Show full text]
  • 1 Diversified Amino Acid-Mediated Allosteric
    Biochemical Journal (2021) 478 2217–2232 https://doi.org/10.1042/BCJ20210191 Research Article Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants Eiji Okamura1,*, Kinuka Ohtaka1,2,3,*, Ryuichi Nishihama4,†, Kai Uchida1, Ayuko Kuwahara1, 5,6,7,8 1,2 Keiichi Mochida and Masami Yokota Hirai Downloaded from http://portlandpress.com/biochemj/article-pdf/478/12/2217/915243/bcj-2021-0191.pdf by guest on 29 September 2021 1Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; 2Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan; 3Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo, Japan; 4Graduate School of Biostudies, Kyoto University, Kyoto, Japan; 5Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan; 6Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan; 7Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, Yokohama, Kanagawa, Japan; 8Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan Correspondence: Masami Yokota Hirai ([email protected]) The phosphorylated pathway of serine biosynthesis is initiated with 3-phosphoglycerate dehydrogenase (PGDH). The liverwort Marchantia polymorpha possesses an amino acid- sensitive MpPGDH which is inhibited by L-serine and activated by five proteinogenic amino acids, while the eudicot Arabidopsis thaliana has amino acid-sensitive AtPGDH1 and AtPGDH3 as well as amino acid-insensitive AtPGDH2. In this study, we analyzed PGDH isozymes of the representative land plants: the monocot Oryza sativa (OsPGDH1– 3), basal angiosperm Amborella trichopoda (AmtriPGDH1–2), and moss Physcomitrium (Physcomitrella) patens (PpPGDH1–4).
    [Show full text]
  • Exploring Modular Allostery Via Interchangeable Regulatory Domains
    Exploring modular allostery via interchangeable regulatory domains Yifei Fana,b, Penelope J. Crossa,b, Geoffrey B. Jamesonc, and Emily J. Parkerb,d,e,1 aBiomolecular Interaction Centre, University of Canterbury, 8140 Christchurch, New Zealand; bDepartment of Chemistry, University of Canterbury, 8140 Christchurch, New Zealand; cMaurice Wilkins Centre, Institute of Fundamental Sciences, Massey University, 4442 Palmerston North, New Zealand; dMaurice Wilkins Centre, Biomolecular Interaction Centre, University of Canterbury, 8140 Christchurch, New Zealand; and eFerrier Research Institute, Victoria University of Wellington, 6140 Wellington, New Zealand Edited by Perry Allen Frey, University of Wisconsin–Madison, Madison, WI, and approved February 8, 2018 (received for review October 12, 2017) Most proteins comprise two or more domains from a limited suite allow formation of prephenate by chorismate mutase (CM) as well of protein families. These domains are often rearranged in various as a series of other important metabolites, including aromatic amino combinations through gene fusion events to evolve new protein acids Phe, Tyr, and Trp (Fig. 1) (15). DAH7PS, situated at the first functions, including the acquisition of protein allostery through committed step of the pathway, is often precisely feedback regu- the incorporation of regulatory domains. The enzyme 3-deoxy-D- lated to control pathway flux in response to metabolic demand via a arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first variety of allosteric strategies in different organisms. This allostery enzyme of aromatic amino acid biosynthesis and displays a diverse ranges from physical gating mechanisms undertaking large confor- range of allosteric mechanisms. DAH7PSs adopt a common archi- mational changes to highly intricate through-protein dynamic net- β α tecture with a shared ( / )8 catalytic domain which can be at- works (16).
    [Show full text]
  • Deciphering the BAR Code of Membrane Modulators
    Cell. Mol. Life Sci. DOI 10.1007/s00018-017-2478-0 Cellular and Molecular LifeSciences REVIEW Deciphering the BAR code of membrane modulators Ulrich Salzer1 · Julius Kostan2 · Kristina Djinović‑Carugo2,3 Received: 30 September 2016 / Revised: 25 January 2017 / Accepted: 27 January 2017 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract The BAR domain is the eponymous domain of Keywords N-BAR domain · F-BAR domain · I-BAR the “BAR-domain protein superfamily”, a large and diverse domain · lipid binding · Membrane remodelling · set of mostly multi-domain proteins that play eminent roles Membrane curvature at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally asso- ciate with lipid membranes and are involved in membrane Introduction sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in Identification of sequence homology between the N-termi- membrane modulating properties. Membrane activities nal regions of the Bin, the amphiphysin, and the yeast Rvs of BAR domains are further modified and regulated by proteins led to the recognition of a novel protein domain intramolecular or inter-subunit domains, by intermolecu- which was named “BAR domain” as an acronym composed lar protein interactions, and by posttranslational modifica- of the first letters of these proteins [1]. This domain was tions. Rather than providing detailed cell biological infor- found in a large set of proteins which were classified as mation on single members of this superfamily, this review BAR domain proteins, later also termed N-BAR domain focuses on biochemical, biophysical, and structural aspects proteins, because several members of this protein family and on recent findings that paradigmatically promote our have an amphipathic helix at the N-terminus of the BAR understanding of processes driven and modulated by BAR domain [2].
    [Show full text]
  • The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation Of
    bioRxiv preprint doi: https://doi.org/10.1101/849810; this version posted January 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 The C-terminal RRM/ACT domain is crucial for fine-tuning the 2 activation of ‘long’ RelA-SpoT Homolog enzymes by ribosomal 3 complexes 4 Hiraku Takada1,2,*, Mohammad Roghanian1,2, Victoriia Murina1,2, Ievgen Dzhygyr1,2, Rikinori 5 Murayama3, Genki Akanuma4, Gemma C. Atkinson1, Abel Garcia-Pino5,6, Vasili Hauryliuk1,2,7* 6 1Department of Molecular Biology, Umeå University, Umeå, Sweden 7 2Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden 8 3Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, 9 Akita, 010-0874, Japan 10 4Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan 11 5Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), 12 Building BC, Room 1C4 203, Boulevard du Triomphe, 1050, Brussels, Belgium 13 6WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium 14 7University of Tartu, Institute of Technology, 50411 Tartu, Estonia 15 16 * Correspondence: 17 Hiraku Takada 18 [email protected] 19 Vasili Hauryliuk 20 [email protected] 21 Keywords: ppGpp1, Rel2, ACT3, RRM4, stringent response5, ribosome6 22 Running title: Rel/RelA regulation by the RRM/ACT domain 23 Abstract: The (p)ppGpp-mediated stringent response is a bacterial stress response implicated in 24 virulence and antibiotic tolerance.
    [Show full text]
  • The Structural Basis of Allosteric Regulation in Proteins
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 583 (2009) 1692–1698 journal homepage: www.FEBSLetters.org Minireview The structural basis of allosteric regulation in proteins Roman A. Laskowski *, Fabian Gerick, Janet M. Thornton European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom article info abstract Article history: Allosteric regulation of protein function occurs when the regulatory trigger, such as the binding of a Received 2 February 2009 small-molecule effector or inhibitor, takes place some distance from the protein’s, or protein com- Revised 5 March 2009 plex’s, active site. This distance can be a few Å, or tens of Å. Many proteins are regulated in this way Accepted 11 March 2009 and exhibit a variety of allosteric mechanisms. Here we review how analyses of experimentally Available online 18 March 2009 determined models of protein 3D structures, using either X-ray crystallography or NMR spectros- Edited by Miguel De la Rosa copy, have revealed some of the mechanisms involved. Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Keywords: Allosteric regulation Protein structure Ligand binding Phosphorylation 1. Introduction tion wherein a small-molecule inhibitor, or indeed another protein molecule, binds to the active site and prevents the protein’s natural Regulation of protein function is crucial to all organisms. Virtu- substrate gaining access. It also differs in that, whereas a compet- ally all processes in the cell need to be carefully controlled and, if itive inhibitor may need to be chemically similar to the substrate in these controls fail, can lead to malfunction and disease.
    [Show full text]