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Olek AT, Rushton PS, Kihara D, Ciesielski P, Aryal UK, Zhang Z, Stauffacher CV, McCann MC, Carpita NC. Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases. PLANT PHYSIOLOGY 2023; 191:142-160. [PMID: 36250895 PMCID: PMC9806608 DOI: 10.1093/plphys/kiac479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/24/2022] [Indexed: 05/05/2023]
Abstract
The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.
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Affiliation(s)
- Anna T Olek
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Phillip S Rushton
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, USA
| | - Peter Ciesielski
- Renewable Resources & Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Uma K Aryal
- Bindley Biosciences Center, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
| | - Zicong Zhang
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, USA
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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Mishra PKK, Nimmanapalli R. In silico characterization of Leptospira interrogans DNA ligase A and delineation of its antimicrobial stretches. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01516-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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3
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Kassem MM, Wang Y, Boomsma W, Lindorff-Larsen K. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation. Biophys J 2017; 110:2342-2348. [PMID: 27276252 DOI: 10.1016/j.bpj.2016.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/28/2022] Open
Abstract
Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.
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Affiliation(s)
- Maher M Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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4
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Zhao J, Beyrakhova K, Liu Y, Alvarez CP, Bueler SA, Xu L, Xu C, Boniecki MT, Kanelis V, Luo ZQ, Cygler M, Rubinstein JL. Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. PLoS Pathog 2017; 13:e1006394. [PMID: 28570695 PMCID: PMC5469503 DOI: 10.1371/journal.ppat.1006394] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/13/2017] [Accepted: 05/01/2017] [Indexed: 12/16/2022] Open
Abstract
Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires’ Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the ‘open’ conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK. V-ATPase-driven acidification of lysosomes in phagocytic cells activates enzymes important for killing of phagocytized pathogens. Successful pathogens can subvert host defenses by secreting effectors that target V-ATPases to inhibit lysosomal acidification or lysosomal fusion with other cell compartments. This study reveals the structure of the V-ATPase:SidK complex, an assembly formed from the interaction of host and pathogen proteins involved in the infection of phagocytic white blood cells by Legionella pneumophila. The structure and activity of the V-ATPase is altered upon SidK binding, providing insight into the infection strategy used by L. pneumophila and possibly other intravacuolar pathogens.
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Affiliation(s)
- Jianhua Zhao
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ksenia Beyrakhova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yao Liu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Claudia P. Alvarez
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Li Xu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Caishuang Xu
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michal T. Boniecki
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (JLR); (MC)
| | - John L. Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (JLR); (MC)
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Ulaganathan T, Boniecki MT, Foran E, Buravenkov V, Mizrachi N, Banin E, Helbert W, Cygler M. New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. ACS Chem Biol 2017; 12:1269-1280. [PMID: 28290654 DOI: 10.1021/acschembio.7b00126] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy ( www.cazy.org ) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV_3936 being one of them. This enzyme cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic acid (IdoA) via a β-elimination mechanism. We report the crystal structure of PLSV_3936 and its complex with a tetrasaccharide substrate. PLSV_3936 folds into a seven-bladed β-propeller, with each blade consisting of four antiparallel β-strands. Sequence conservation analysis identified a highly conserved region lining at one end of a deep crevice on the protein surface. The putative active site was identified by mutagenesis and activity measurements. Crystal structure of the enzyme with a bound tetrasaccharide substrate confirmed the identity of base and acid residues and allowed determination of the catalytic mechanism and also the identification of residues neutralizing the uronic acid carboxylic group. The PLSV_3936 structure provides an example of a convergent evolution among polysaccharide lyases toward a common active site architecture embedded in distinct folds.
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Affiliation(s)
| | - Michal T. Boniecki
- Department
of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Elizabeth Foran
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Vitaliy Buravenkov
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Naama Mizrachi
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Ehud Banin
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - William Helbert
- Recherches
sur les Macromolécules Végétales, UPR-CNRS 5301, Université Joseph Fourier, and Institut de Chimie Moléculaire de Grenoble, ICMG, FR-CNRS
2607, Grenoble, France
| | - Miroslaw Cygler
- Department
of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department
of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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6
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Kim YJ, Yoo WG, Lee MR, Kang JM, Na BK, Cho SH, Park MY, Ju JW. Molecular and Structural Characterization of the Tegumental 20.6-kDa Protein in Clonorchis sinensis as a Potential Druggable Target. Int J Mol Sci 2017; 18:E557. [PMID: 28273846 PMCID: PMC5372573 DOI: 10.3390/ijms18030557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/24/2017] [Accepted: 02/28/2017] [Indexed: 11/17/2022] Open
Abstract
The tegument, representing the membrane-bound outer surface of platyhelminth parasites, plays an important role for the regulation of the host immune response and parasite survival. A comprehensive understanding of tegumental proteins can provide drug candidates for use against helminth-associated diseases, such as clonorchiasis caused by the liver fluke Clonorchis sinensis. However, little is known regarding the physicochemical properties of C. sinensis teguments. In this study, a novel 20.6-kDa tegumental protein of the C. sinensis adult worm (CsTegu20.6) was identified and characterized by molecular and in silico methods. The complete coding sequence of 525 bp was derived from cDNA clones and encodes a protein of 175 amino acids. Homology search using BLASTX showed CsTegu20.6 identity ranging from 29% to 39% with previously-known tegumental proteins in C. sinensis. Domain analysis indicated the presence of a calcium-binding EF-hand domain containing a basic helix-loop-helix structure and a dynein light chain domain exhibiting a ferredoxin fold. We used a modified method to obtain the accurate tertiary structure of the CsTegu20.6 protein because of the unavailability of appropriate templates. The CsTegu20.6 protein sequence was split into two domains based on the disordered region, and then, the structure of each domain was modeled using I-TASSER. A final full-length structure was obtained by combining two structures and refining the whole structure. A refined CsTegu20.6 structure was used to identify a potential CsTegu20.6 inhibitor based on protein structure-compound interaction analysis. The recombinant proteins were expressed in Escherichia coli and purified by nickel-nitrilotriacetic acid affinity chromatography. In C. sinensis, CsTegu20.6 mRNAs were abundant in adult and metacercariae, but not in the egg. Immunohistochemistry revealed that CsTegu20.6 localized to the surface of the tegument in the adult fluke. Collectively, our results contribute to a better understanding of the structural and functional characteristics of CsTegu20.6 and homologs of flukes. One compound is proposed as a putative inhibitor of CsTegu20.6 to facilitate further studies for anthelmintics.
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Affiliation(s)
- Yu-Jung Kim
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
| | - Won Gi Yoo
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
| | - Myoung-Ro Lee
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju 52727, Korea.
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju 52727, Korea.
| | - Shin-Hyeong Cho
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
| | - Mi-Yeoun Park
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
| | - Jung-Won Ju
- Division of Malaria and Parasitic Diseases, Centre for Immunology and Pathology, Korea National Research Institute of Health, Chungbuk 28159, Korea.
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Roy SS, Kapoor M. In silico identification and computational analysis of the nucleotide binding site in the C-terminal domain of Hsp90. J Mol Graph Model 2016; 70:253-274. [PMID: 27771574 DOI: 10.1016/j.jmgm.2016.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/02/2016] [Indexed: 12/28/2022]
Abstract
Hsp90 contains two distinct Nucleotide Binding Sites (NBS), in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. The NTD site belongs to the GHKL super-family of ATPases and has been the subject of extensive characterization. However, a structure of the nucleotide-bound form of CTD is still unavailable. In this study molecular modeling was employed to incorporate experimental data using partial constructs of the CTD, from work published by many research groups, onto existing structural models of its apo- form. Our attempts to locate potential nucleotide ligand-binding sites or cavities yielded one major candidate-a structurally unconventional site-exhibiting the requisite shape and volume for accommodation of tri-phosphate nucleotides. Its structure was refined by molecular dynamics (MD)-based techniques. We reproducibly docked the Mg2+ complexed form of ATP, GTP, CTP, TTP and UTP to this putative NBS. These docking simulations and calculated ligand-binding scores are in general agreement with published data about experimentally measured binding to the CTD. The overall pattern of interactions between residues lining the site and docked nucleotides is conserved and broadly similar to that of other nucleotide-binding sites. Our docking simulations suggest that nucleotide binding stabilizes the only structurally labile region, thereby providing a rationale for the increased resistance to thermal denaturation and proteolysis. The docked nucleotides do not intrude onto the surface of residues involved in dimerization or chaperoning. Our molecular modeling permitted recognition of larger structural changes in the nucleotide-bound CTD dimer, including stabilization of helix-2 in both chains and intra- and inter- chain interactions between three residues (I613, Q617, R620).
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Affiliation(s)
- Samir S Roy
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Manju Kapoor
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
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Ashby C, Johnson D, Walker K, Kanj IA, Xia G, Huang X. New enumeration algorithm for protein structure comparison and classification. BMC Genomics 2013; 14 Suppl 2:S1. [PMID: 23445440 PMCID: PMC3582452 DOI: 10.1186/1471-2164-14-s2-s1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches for protein structure comparison apply the secondary structure elements (SSEs) representation of protein structures. RESULTS We study the complexity of the protein structure comparison problem based on a mixed-graph model with respect to different computational frameworks. We develop an effective approach for protein structure comparison based on a novel independent set enumeration algorithm. Our approach (named: ePC, efficient enumeration-based Protein structure Comparison) is tested for general purpose protein structure comparison as well as for specific protein examples. Compared with other graph-based approaches for protein structure comparison, the theoretical running-time O(1.47 rnn2) of our approach ePC is significantly better, where n is the smaller number of SSEs of the two proteins, r is a parameter of small value. CONCLUSION Through the enumeration algorithm, our approach can identify different substructures from a list of high-scoring solutions of biological interest. Our approach is flexible to conduct protein structure comparison with the SSEs in sequential and non-sequential order as well. Supplementary data of additional testing and the source of ePC will be available at http://bioinformatics.astate.edu/.
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Affiliation(s)
- Cody Ashby
- Molecular Bioscience Graduate Program, Arkansas State University, Arkansas, USA
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9
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Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnol Adv 2012; 31:925-35. [PMID: 23280013 DOI: 10.1016/j.biotechadv.2012.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 12/09/2012] [Accepted: 12/23/2012] [Indexed: 02/05/2023]
Abstract
Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing 'big' biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.
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Ritchie DW, Ghoorah AW, Mavridis L, Venkatraman V. Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity. Bioinformatics 2012; 28:3274-81. [DOI: 10.1093/bioinformatics/bts618] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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11
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Homology modeling and analysis of structure predictions of the bovine rhinitis B virus RNA dependent RNA polymerase (RdRp). Int J Mol Sci 2012; 13:8998-9013. [PMID: 22942748 PMCID: PMC3430279 DOI: 10.3390/ijms13078998] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/03/2012] [Accepted: 07/11/2012] [Indexed: 11/16/2022] Open
Abstract
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp), which is also known as 3D polymerase (3Dpol). In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3Dpol using a combination of different computational tools. Model structures of BRBV 3Dpol were verified for their stereochemical quality and accuracy. The BRBV 3Dpol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P), nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3Dpol (PDB, 1U09 and 2E9Z). The closest proximity of BRBV and FMDV 3Dpol as compared to human rhinovirus type 16 (HRV-16) and rabbit hemorrhagic disease virus (RHDV) 3Dpols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD) between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3Dpol compared to FMDV 3Dpol, indicate that despite a very high homology to FMDV 3Dpol, BRBV 3Dpol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the design of structure-function interventions and identification of molecular targets for drug design applicable to Aphthovirus RdRps.
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Gelly JC, Joseph AP, Srinivasan N, de Brevern AG. iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res 2011; 39:W18-23. [PMID: 21586582 PMCID: PMC3125758 DOI: 10.1093/nar/gkr333] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman–Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of ∼88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA+ in >80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient ‘sequence-based’ structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.
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Affiliation(s)
- Jean-Christophe Gelly
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Université Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France
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