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Construction and Loss of Bacterial Flagellar Filaments
biomolecules Review Construction and Loss of Bacterial Flagellar Filaments Xiang-Yu Zhuang and Chien-Jung Lo * Department of Physics and Graduate Institute of Biophysics, National Central University, Taoyuan City 32001, Taiwan; [email protected] * Correspondence: [email protected] Received: 31 July 2020; Accepted: 4 November 2020; Published: 9 November 2020 Abstract: The bacterial flagellar filament is an extracellular tubular protein structure that acts as a propeller for bacterial swimming motility. It is connected to the membrane-anchored rotary bacterial flagellar motor through a short hook. The bacterial flagellar filament consists of approximately 20,000 flagellins and can be several micrometers long. In this article, we reviewed the experimental works and models of flagellar filament construction and the recent findings of flagellar filament ejection during the cell cycle. The length-dependent decay of flagellar filament growth data supports the injection-diffusion model. The decay of flagellar growth rate is due to reduced transportation of long-distance diffusion and jamming. However, the filament is not a permeant structure. Several bacterial species actively abandon their flagella under starvation. Flagellum is disassembled when the rod is broken, resulting in an ejection of the filament with a partial rod and hook. The inner membrane component is then diffused on the membrane before further breakdown. These new findings open a new field of bacterial macro-molecule assembly, disassembly, and signal transduction. Keywords: self-assembly; injection-diffusion model; flagellar ejection 1. Introduction Since Antonie van Leeuwenhoek observed animalcules by using his single-lens microscope in the 18th century, we have entered a new era of microbiology. -
Covalent Flexible Peptide Docking in Rosetta
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.06.441297; this version posted May 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. Covalent Flexible Peptide Docking in Rosetta Barr Tivon1,#, Ronen Gabizon1,#, Bente A. Somsen2, Peter J. Cossar2, Christian Ottmann2 , Nir London1,* 1 Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel 2 Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands # equal contribution * Corresponding author: [email protected] Keywords: Covalent peptides; peptide docking; CovPepDock; FlexPepDock; 14-3-3; Electrophilic peptides; bioRxiv preprint doi: https://doi.org/10.1101/2021.05.06.441297; this version posted May 6, 2021. 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-NC-ND 4.0 International license. Abstract Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides, for which it produced a top-five scoring, near-native model, in 89% and 100% of the cases, respectively. -
A Global Review on Short Peptides: Frontiers and Perspectives †
molecules Review A Global Review on Short Peptides: Frontiers and Perspectives † Vasso Apostolopoulos 1 , Joanna Bojarska 2,* , Tsun-Thai Chai 3 , Sherif Elnagdy 4 , Krzysztof Kaczmarek 5 , John Matsoukas 1,6,7, Roger New 8,9, Keykavous Parang 10 , Octavio Paredes Lopez 11 , Hamideh Parhiz 12, Conrad O. Perera 13, Monica Pickholz 14,15, Milan Remko 16, Michele Saviano 17, Mariusz Skwarczynski 18, Yefeng Tang 19, Wojciech M. Wolf 2,*, Taku Yoshiya 20 , Janusz Zabrocki 5, Piotr Zielenkiewicz 21,22 , Maha AlKhazindar 4 , Vanessa Barriga 1, Konstantinos Kelaidonis 6, Elham Mousavinezhad Sarasia 9 and Istvan Toth 18,23,24 1 Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; [email protected] (V.A.); [email protected] (J.M.); [email protected] (V.B.) 2 Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego˙ 116, 90-924 Lodz, Poland 3 Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia; [email protected] 4 Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; [email protected] (S.E.); [email protected] (M.A.) 5 Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego˙ 116, 90-924 Lodz, Poland; [email protected] (K.K.); [email protected] (J.Z.) 6 NewDrug, Patras Science Park, 26500 Patras, Greece; [email protected] 7 Department of Physiology and Pharmacology, -
RT² Profiler PCR Array (96-Well Format and 384-Well [4 X 96] Format)
RT² Profiler PCR Array (96-Well Format and 384-Well [4 x 96] Format) Human Toll-Like Receptor Signaling Pathway Cat. no. 330231 PAHS-018ZA For pathway expression analysis Format For use with the following real-time cyclers RT² Profiler PCR Array, Applied Biosystems® models 5700, 7000, 7300, 7500, Format A 7700, 7900HT, ViiA™ 7 (96-well block); Bio-Rad® models iCycler®, iQ™5, MyiQ™, MyiQ2; Bio-Rad/MJ Research Chromo4™; Eppendorf® Mastercycler® ep realplex models 2, 2s, 4, 4s; Stratagene® models Mx3005P®, Mx3000P®; Takara TP-800 RT² Profiler PCR Array, Applied Biosystems models 7500 (Fast block), 7900HT (Fast Format C block), StepOnePlus™, ViiA 7 (Fast block) RT² Profiler PCR Array, Bio-Rad CFX96™; Bio-Rad/MJ Research models DNA Format D Engine Opticon®, DNA Engine Opticon 2; Stratagene Mx4000® RT² Profiler PCR Array, Applied Biosystems models 7900HT (384-well block), ViiA 7 Format E (384-well block); Bio-Rad CFX384™ RT² Profiler PCR Array, Roche® LightCycler® 480 (96-well block) Format F RT² Profiler PCR Array, Roche LightCycler 480 (384-well block) Format G RT² Profiler PCR Array, Fluidigm® BioMark™ Format H Sample & Assay Technologies Description The Human Toll-Like Receptor (TLR) Signaling Pathway RT² Profiler PCR Array profiles the expression of 84 genes central to TLR-mediated signal transduction and innate immunity. The TLR family of pattern recognition receptors (PRRs) detects a wide range of bacteria, viruses, fungi and parasites via pathogen-associated molecular patterns (PAMPs). Each receptor binds to specific ligands, initiates a tailored innate immune response to the specific class of pathogen, and activates the adaptive immune response. -
Human Alkaline Phosphatase Dephosphorylates Microbial Products and Is Elevated in Preterm Neonates with a History of Late-Onset Sepsis
RESEARCH ARTICLE Human alkaline phosphatase dephosphorylates microbial products and is elevated in preterm neonates with a history of late-onset sepsis Matthew Pettengill1,2, Juan D. Matute2, Megan Tresenriter3, Julie Hibbert4, David Burgner5,6,7, Peter Richmond6, Jose Luis MillaÂn8, Al Ozonoff2, Tobias Strunk4, Andrew Currie4,9, Ofer Levy1,2* a1111111111 a1111111111 1 Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, United States of America, 2 Harvard Medical School, Boston, Massachusetts, United States a1111111111 of America, 3 University of California Davis School of Medicine, Davis, California, United States of America, a1111111111 4 The University of Western Australia, Crawley, Western Australia, Australia, 5 Murdoch Children's a1111111111 Research Institute, Parkville, Victoria, Australia, 6 Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia, 7 Department of Paediatrics, Monash University, Clayton, Victoria, Australia, 8 Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, LaJolla, California, United States of America, 9 School of Veterinary & Life Sciences, Murdoch University, Murdoch, Western Australia, Australia OPEN ACCESS * [email protected] Citation: Pettengill M, Matute JD, Tresenriter M, Hibbert J, Burgner D, Richmond P, et al. (2017) Human alkaline phosphatase dephosphorylates Abstract microbial products and is elevated in preterm neonates with a history of late-onset sepsis. PLoS ONE 12(4): e0175936. https://doi.org/10.1371/ journal.pone.0175936 Background Editor: Olivier Baud, Hopital Robert Debre, FRANCE A host defense function for Alkaline phosphatases (ALPs) is suggested by the contribution of intestinal ALP to detoxifying bacterial lipopolysaccharide (endotoxin) in animal models in Received: July 6, 2016 vivo and the elevation of ALP activity following treatment of human cells with inflammatory Accepted: April 3, 2017 stimuli in vitro. -
A Technology Platform to Test the Efficacy of Purification of Alginate
Materials 2014, 7, 2087-2103; doi:10.3390/ma7032087 OPEN ACCESS materials ISSN 1996-1944 www.mdpi.com/journal/materials Article A Technology Platform to Test the Efficacy of Purification of Alginate Genaro A. Paredes-Juarez *, Bart J. de Haan, Marijke M. Faas and Paul de Vos Department of Pathology and Medical Biology, Section of Immunoendocrinology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, EA11, 9700 RB Groningen, The Netherlands; E-Mails: [email protected] (B.J.H.); [email protected] (M.M.F.); [email protected] (P.V.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +31-50-3615-180; Fax: 31-50-3619-911. Received: 10 January 2014; in revised form: 12 February 2014 / Accepted: 5 March 2014 / Published: 12 March 2014 Abstract: Alginates are widely used in tissue engineering technologies, e.g., in cell encapsulation, in drug delivery and various immobilization procedures. The success rates of these studies are highly variable due to different degrees of tissue response. A cause for this variation in success is, among other factors, its content of inflammatory components. There is an urgent need for a technology to test the inflammatory capacity of alginates. Recently, it has been shown that pathogen-associated molecular patterns (PAMPs) in alginate are potent immunostimulatories. In this article, we present the design and evaluation of a technology platform to assess (i) the immunostimulatory capacity of alginate or its contaminants, (ii) where in the purification process PAMPs are removed, and (iii) which Toll-like receptors (TLRs) and ligands are involved. -
An Immunologist's Perspective on Nutrition, Immunity, and Infectious
© 2009 Poultry Science Association, Inc. An immunologist’s perspective on nutrition, immunity, and infectious diseases: 1 Introduction and overview M. H. Kogut *2 and K. Klasing † * Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX 77845; and † Department of Avian Sciences, University of California, Davis 95616 Primary Audience: Poultry Nutritionists, Immunologists, Veterinarians, Researchers SUMMARY The immune system is a multifaceted arrangement of membranes (skin, epithelial, and mucus), cells, and molecules whose function is to eradicate invading pathogens or cancer cells from a host. Working together, the various components of the immune system perform a balancing act of being lethal enough to kill pathogens or cancer cells yet specific so as not to cause extensive damage to “self” tissues of the host. A functional immune system is a requirement of a healthy life in modern animal production. Yet infectious diseases still represent a serious drain on the economics (reduced production, cost of therapeutics, and vaccines) and welfare of animal agriculture. The interaction involving nutrition and immunity and how the host deals with infectious agents is a strategic deter- minant in animal health. Almost all nutrients in the diet play a fundamental role in sustaining an op- timal immune response, such that deficient and excessive intakes can have negative consequences on immune status and susceptibility to a variety of pathogens. Dietary components can regulate physiological functions of the body; interacting with the immune response is one of the most im- portant functions of nutrients. The pertinent question to be asked and answered in the current era of poultry production is whether the level of nutrients that maximizes production in commercial diets is sufficient to maintain competence of immune status and disease resistance. -
1 Design and Production of Specifically and with High Affinity
1 Design and Production of Specifically and with High Affinity Reacting Peptides (SHARP®-s) by Jan C Biro HOMULUS FOUNDATION, 612 S. Flower Str., #1220, 90017 CA, USA [email protected] www.janbiro.com 2 Abstract Background A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests that significant number of amino acids in specifically interacting proteins are coded by partially complementary codons. It means that the 1st and 3rd residues of codons coding many co-locating amino acids are complementary but the 2nd may but not necessarily complementary: like 5’-AXG-3’/3’-CXT-5’ codon pair, where X is any nucleotide. Results A mixture of 45 residue long, reverse, partially complementary oligonucleotide sequences (target pool) were synthesized to selected epitopes of query mRNA sequences. The 2nd codon residues were randomized. The target oligonucleotide pool was inserted into vectors, expressed and the protein products were screened for affinity to the query in Bacterial Two-Hybrid System. The best clones were used for larger-scale protein syntheses and characterization. It was possible to design and produce specific and with high affinity reacting (Kd: ~100 nM) oligopeptide reagents to GAL4 query oligopeptides. Conclusions Second codon residue randomization is a promising method to design and produce affinity peptides to any protein sequences. The method has the potential to be a rapid, inexpensive, high throughput, non-immunoglobulin based alternative to recent in vivo antibody generating procedures. -
Crystal Structure of Bacillus Cereus Flagellin and Structure-Guided Fusion-Protein Designs
www.nature.com/scientificreports OPEN Crystal structure of Bacillus cereus fagellin and structure-guided fusion-protein designs Received: 6 February 2018 Meong Il Kim1, Choongdeok Lee1, Jaewan Park1, Bo-Young Jeon2 & Minsun Hong1 Accepted: 23 March 2018 Flagellin is a major component of the fagellar flament. Flagellin also functions as a specifc ligand Published: xx xx xxxx that stimulates innate immunity through direct interaction with Toll-like receptor 5 (TLR5) in the host. Because fagellin activates the immune response, it has been of interest to develop as a vaccine adjuvant in subunit vaccines or antigen fusion vaccines. Despite the widespread application of fagellin fusion in preventing infectious diseases, fagellin-antigen fusion designs have never been biophysically and structurally characterized. Moreover, fagellin from Salmonella species has been used extensively despite containing hypervariable regions not required for TLR5 that can cause an unexpected immune response. In this study, fagellin from Bacillus cereus (BcFlg) was identifed as the smallest fagellin molecule containing only the conserved TLR5-activating D0 and D1 domains. The crystal structure of BcFlg was determined to provide a scheme for fusion designs. Through homology-based modeling and comparative structural analyses, diverse fusion strategies were proposed. Moreover, cellular and biophysical analysis of an array of fusion constructs indicated that insertion fusion at BcFlg residues 178–180 does not interfere with the protein stability or TLR5-stimulating capacity of fagellin, suggesting its usefulness in the development and optimization of fagellin fusion vaccines. Flagella enable bacterial locomotion toward favorable conditions or away from unfavorable environments. Te bacterial fagellum transverses from the cytoplasm to the outside of the bacterium and comprises more than 30 diferent proteins1,2. -
DNA Vaccine-Encoded Flagellin Can Be Used As an Adjuvant Scaffold to Augment HIV-1 Gp41 Membrane Proximal External Region Immunogenicity
viruses Article DNA Vaccine-Encoded Flagellin Can Be Used as an Adjuvant Scaffold to Augment HIV-1 gp41 Membrane Proximal External Region Immunogenicity Lara Ajamian 1,2, Luca Melnychuk 1,2, Patrick Jean-Pierre 1 and Gerasimos J. Zaharatos 1,3,* ID 1 Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; [email protected] (L.A.); [email protected] (L.M.); [email protected] (P.J.-P.) 2 Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada 3 Division of Infectious Disease, Department of Medicine & Division of Medical Microbiology, Department of Clinical Laboratory Medicine, Jewish General Hospital, Montréal, QC H3T 1E2, Canada * Correspondence: [email protected]; Tel.: +1-514-340-8294 Received: 28 January 2018; Accepted: 23 February 2018; Published: 27 February 2018 Abstract: Flagellin’s potential as a vaccine adjuvant has been increasingly explored over the last three decades. Monomeric flagellin proteins are the only known agonists of Toll-like receptor 5 (TLR5). This interaction evokes a pro-inflammatory state that impacts upon both innate and adaptive immunity. While pathogen associated molecular patterns (PAMPs) like flagellin have been used as stand-alone adjuvants that are co-delivered with antigen, some investigators have demonstrated a distinct advantage to incorporating antigen epitopes within the structure of flagellin itself. This approach has been particularly effective in enhancing humoral immune responses. We sought to use flagellin as both scaffold and adjuvant for HIV gp41 with the aim of eliciting antibodies to the membrane proximal external region (MPER). -
Activation of Toll-Like Receptor 5 on Breast Cancer Cells by Flagellin Suppresses Cell Proliferation and Tumor Growth
Published OnlineFirst March 22, 2011; DOI: 10.1158/0008-5472.CAN-10-1993 Cancer Microenvironment and Immunology Research Activation of Toll-like Receptor 5 on Breast Cancer Cells by Flagellin Suppresses Cell Proliferation and Tumor Growth Zhenyu Cai, Amir Sanchez, Zhongcheng Shi, Tingting Zhang, Mingyao Liu, and Dekai Zhang Abstract Increasing evidence showed that Toll-like receptors (TLR), key receptors in innate immunity, play a role in cancer progression and development but activation of different TLRs might exhibit the exact opposite outcome, antitumor or protumor effects. TLR function has been extensively studied in innate immune cells, so we investigated the role of TLR signaling in breast cancer epithelial cells. We found that TLR5 was highly expressed in breast carcinomas and that TLR5 signaling pathway is overly responsive in breast cancer cells. Interestingly, flagellin/TLR5 signaling in breast cancer cells inhibits cell proliferation and an anchorage-independent growth, a hallmark of tumorigenic transformation. In addition, the secretion of soluble factors induced by flagellin contributed to the growth-inhibitory activity in an autocrine fashion. The inhibitory activity was further confirmed in mouse xenografts of human breast cancer cells. These findings indicate that TLR5 activation by flagellin mediates innate immune response to elicit potent antitumor activity in breast cancer cells themselves, which may serve as a novel therapeutic target for human breast cancer therapy. Cancer Res; 71(7); 1–10. Ó2011 AACR. Introduction (16, 17). Thus, the function and biological importance of TLRs expressed on various tumor cells seem complex. Toll-like receptors (TLR) are membrane-bound receptors Unlike other TLR family members, TLR5 is not expressed on that play key roles in both the innate and adaptive immune mouse macrophages and conventional dendritic cells (DC). -
Bacterial Flagellin—A Potent Immunomodulatory Agent
OPEN Experimental & Molecular Medicine (2017) 49, e373; doi:10.1038/emm.2017.172 Official journal of the Korean Society for Biochemistry and Molecular Biology www.nature.com/emm REVIEW Bacterial flagellin—a potent immunomodulatory agent Irshad A Hajam1, Pervaiz A Dar2, Imam Shahnawaz2, Juan Carlos Jaume2 and John Hwa Lee1 Flagellin is a subunit protein of the flagellum, a whip-like appendage that enables bacterial motility. Traditionally, flagellin was viewed as a virulence factor that contributes to the adhesion and invasion of host cells, but now it has emerged as a potent immune activator, shaping both the innate and adaptive arms of immunity during microbial infections. In this review, we summarize our understanding of bacterial flagellin and host immune system interactions and the role flagellin as an adjuvant, anti-tumor and radioprotective agent, and we address important areas of future research interests. Experimental & Molecular Medicine (2017) 49, e373; doi:10.1038/emm.2017.172; published online 1 September 2017 INTRODUCTION vaccines. Even though all the adjuvants studied so far have The immune system has evolved to fight off microbial invasion proven to be effective, flagellin, a TLR5 agonist, has been through the coordinated action of the innate and adaptive arms shown more promising results without any major side effects. of the immunity. Innate immune cells respond to a variety of Flagellin is the structural component of the flagellum, a stimuli, including bacterial, viral, parasitic or fungal infections, locomotory organ that is mostly associated with Gram-negative via members of structurally related receptors termed toll-like bacteria. It is characterized by highly conserved N- and receptors (TLRs).