51
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Antlion optimization algorithm for pairwise structural alignment with bi-objective functions. Neural Comput Appl 2019. [DOI: 10.1007/s00521-019-04176-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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52
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Yin X, Li W, Ma H, Zeng W, Peng C, Li Y, Liu M, Chen Q, Zhou R, Jin T. Crystal structure and activation mechanism of DR3 death domain. FEBS J 2019; 286:2593-2610. [PMID: 30941855 DOI: 10.1111/febs.14834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/01/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Death receptor 3 (DR3) (a.k.a. tumor necrosis factor receptor superfamily 25) plays a key role in the immune system by activating nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway. Here we present the crystal structures of human and mouse DR3 intracellular death domain (DD) at 2.7 and 2.5 Å resolutions, respectively. The mouse DR3 DD adopts a classical six-helix bundle structure while human DR3 DD displays an extended fold. Though there is one-amino-acid difference in the linker between maltose-binding protein (MBP) tag and DR3 DD, according to our self-interaction analysis, the hydrophobic interface discovered in MBP-hDR3 DD crystal structure is responsible for both hDR3 DD and mDR3 DD homotypic interaction. Furthermore, our biochemical analysis indicates that the sequence variation between human and mouse DR3 DD does not affect its structure and function. Small-angle X-ray scattering analysis shows the averaged solution structures of both human and mouse MBP-DR3 DD are the combination of different conformations with different proportion. Through switching to the open conformation, DR3 DD could improve the interaction with downstream element TNFR-associated death domain (TRADD). Here we propose an activation-dependent structural rearrangement model: the DD region is folded as the six-helix bundles in the resting state, while upon extracellular ligand engagement, it switches to the open conformation, which facilitates its self-association and the recruitment of TRADD. Our results provide detailed insights into the architecture of DR3 DD and the molecular mechanism of activation. DATABASES: All refined structure coordinates as well as the corresponding structure factors have been deposited in the PDB under the accession codes 5YGS, 5YEV, 5YGP, 5ZNY, 5ZNZ.
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Affiliation(s)
- Xueying Yin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Wenqian Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Huan Ma
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Weihong Zeng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Chao Peng
- Zhangjiang Lab, National Facility for Protein Science in Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yajuan Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Muziying Liu
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Quan Chen
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongbin Zhou
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai, China
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53
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RUPEE: A fast and accurate purely geometric protein structure search. PLoS One 2019; 14:e0213712. [PMID: 30875409 PMCID: PMC6420038 DOI: 10.1371/journal.pone.0213712] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022] Open
Abstract
Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these limitations we have developed RUPEE, a fast and accurate purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results. The RUPEE protein structure search is available at https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
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54
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Kaiser F, Labudde D. Unsupervised Discovery of Geometrically Common Structural Motifs and Long-Range Contacts in Protein 3D Structures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:671-680. [PMID: 29990265 DOI: 10.1109/tcbb.2017.2786250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The essential role of small evolutionarily conserved structural units in proteins has been extensively researched and validated. A popular example are serine proteases, where the peptide cleavage reaction is realized by a configuration of only three residues. Brought to spatial proximity during the protein folding process, such structural motifs are often long-range contacts and usually hard to detect at sequence level. Due to the constantly increasing resource of protein 3D structure data, the computational identification of structural motifs can contribute significantly to the understanding of protein fold and function. Thus, we propose a method to discover structural motifs of high geometrical similarity and desired sequence separation in protein 3D structure data. By utilizing methods originated from data mining, no a priori knowledge is required. The applicability of the method is demonstrated by the identification of the catalytic unit of serine proteases and the ion-coordination center of cupredoxins. Furthermore, large-scale analysis of the entire Protein Data Bank points towards the presence of ubiquitous structural motifs, independent of any specific fold or function. We envision that our method is suitable to uncover functional mechanisms and to derive fingerprint libraries of structural motifs, which could be used to assess protein family association.
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55
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Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes: first investigation of a class F sortase. Biochem J 2019; 476:665-682. [PMID: 30670573 DOI: 10.1042/bcj20180885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/17/2022]
Abstract
Sortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A-F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody-drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications.
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56
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Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment. Molecules 2019; 24:molecules24010179. [PMID: 30621295 PMCID: PMC6337464 DOI: 10.3390/molecules24010179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/29/2018] [Accepted: 01/01/2019] [Indexed: 11/16/2022] Open
Abstract
Calculation of structural features of proteins, nucleic acids, and nucleic acid-protein complexes on the basis of their geometries and studying various interactions within these macromolecules, for which high-resolution structures are stored in Protein Data Bank (PDB), require parsing and extraction of suitable data stored in text files. To perform these operations on large scale in the face of the growing amount of macromolecular data in public repositories, we propose to perform them in the distributed environment of Azure Data Lake and scale the calculations on the Cloud. In this paper, we present dedicated data extractors for PDB files that can be used in various types of calculations performed over protein and nucleic acids structures in the Azure Data Lake. Results of our tests show that the Cloud storage space occupied by the macromolecular data can be successfully reduced by using compression of PDB files without significant loss of data processing efficiency. Moreover, our experiments show that the performed calculations can be significantly accelerated when using large sequential files for storing macromolecular data and by parallelizing the calculations and data extractions that precede them. Finally, the paper shows how all the calculations can be performed in a declarative way in U-SQL scripts for Data Lake Analytics.
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57
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Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes. BMC Evol Biol 2018; 18:194. [PMID: 30563447 PMCID: PMC6299612 DOI: 10.1186/s12862-018-1302-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Venom-expressed sphingomyelinase D/phospholipase D (SMase D/PLD) enzymes evolved from the ubiquitous glycerophosphoryl diester phosphodiesterases (GDPD). Expression of GDPD-like SMaseD/PLD toxins in both arachnids and bacteria has inspired consideration of the relative contributions of lateral gene transfer and convergent recruitment in the evolutionary history of this lineage. Previous work recognized two distinct lineages, a SicTox-like (ST-like) clade including the arachnid toxins, and an Actinobacterial-toxin like (AT-like) clade including the bacterial toxins and numerous fungal homologs. Results Here we expand taxon sampling by homology detection to discover new GDPD-like SMase D/PLD homologs. The ST-like clade now includes homologs in a wider variety of arthropods along with a sister group in Cnidaria; the AT-like clade now includes additional fungal phyla and proteobacterial homologs; and we report a third clade expressed in diverse aquatic metazoan taxa, a few single-celled eukaryotes, and a few aquatic proteobacteria. GDPD-like SMaseD/PLDs have an ancient presence in chelicerates within the ST-like family and ctenophores within the Aquatic family. A rooted phylogenetic tree shows that the three clades derived from a basal paraphyletic group of proteobacterial GDPD-like SMase D/PLDs, some of which are on mobile genetic elements. GDPD-like SMase D/PLDs share a signature C-terminal motif and a shortened βα1 loop, features that distinguish them from GDPDs. The three major clades also have active site loop signatures that distinguish them from GDPDs and from each other. Analysis of molecular phylogenies with respect to organismal relationships reveals a dynamic evolutionary history including both lateral gene transfer and gene duplication/loss. Conclusions The GDPD-like SMaseD/PLD enzymes derive from a single ancient ancestor, likely proteobacterial, and radiated into diverse organismal lineages at least in part through lateral gene transfer. Electronic supplementary material The online version of this article (10.1186/s12862-018-1302-2) contains supplementary material, which is available to authorized users.
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58
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Alnasir JJ, Shanahan HP. The application of Hadoop in structural bioinformatics. Brief Bioinform 2018; 21:96-105. [PMID: 30462158 DOI: 10.1093/bib/bby106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/20/2018] [Accepted: 10/05/2018] [Indexed: 11/13/2022] Open
Abstract
The paper reviews the use of the Hadoop platform in structural bioinformatics applications. For structural bioinformatics, Hadoop provides a new framework to analyse large fractions of the Protein Data Bank that is key for high-throughput studies of, for example, protein-ligand docking, clustering of protein-ligand complexes and structural alignment. Specifically we review in the literature a number of implementations using Hadoop of high-throughput analyses and their scalability. We find that these deployments for the most part use known executables called from MapReduce rather than rewriting the algorithms. The scalability exhibits a variable behaviour in comparison with other batch schedulers, particularly as direct comparisons on the same platform are generally not available. Direct comparisons of Hadoop with batch schedulers are absent in the literature but we note there is some evidence that Message Passing Interface implementations scale better than Hadoop. A significant barrier to the use of the Hadoop ecosystem is the difficulty of the interface and configuration of a resource to use Hadoop. This will improve over time as interfaces to Hadoop, e.g. Spark improve, usage of cloud platforms (e.g. Azure and Amazon Web Services (AWS)) increases and standardised approaches such as Workflow Languages (i.e. Workflow Definition Language, Common Workflow Language and Nextflow) are taken up.
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Affiliation(s)
- Jamie J Alnasir
- Institute of Cancer Research, Old Brompton Road, London, United Kingdom
| | - Hugh P Shanahan
- Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
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59
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Hooper WF, Walcott BD, Wang X, Bystroff C. Fast design of arbitrary length loops in proteins using InteractiveRosetta. BMC Bioinformatics 2018; 19:337. [PMID: 30249181 PMCID: PMC6154894 DOI: 10.1186/s12859-018-2345-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background With increasing interest in ab initio protein design, there is a desire to be able to fully explore the design space of insertions and deletions. Nature inserts and deletes residues to optimize energy and function, but allowing variable length indels in the context of an interactive protein design session presents challenges with regard to speed and accuracy. Results Here we present a new module (INDEL) for InteractiveRosetta which allows the user to specify a range of lengths for a desired indel, and which returns a set of low energy backbones in a matter of seconds. To make the loop search fast, loop anchor points are geometrically hashed using C α-C α and C β-C β distances, and the hash is mapped to start and end points in a pre-compiled random access file of non-redundant, protein backbone coordinates. Loops with superposable anchors are filtered for collisions and returned to InteractiveRosetta as poly-alanine for display and selective incorporation into the design template. Sidechains can then be added using RosettaDesign tools. Conclusions INDEL was able to find viable loops in 100% of 500 attempts for all lengths from 3 to 20 residues. INDEL has been applied to the task of designing a domain-swapping loop for T7-endonuclease I, changing its specificity from Holliday junctions to paranemic crossover (PX) DNA. Electronic supplementary material The online version of this article (10.1186/s12859-018-2345-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William F Hooper
- Emmes Corporation, Rockville, Washington, MD, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | | | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Christopher Bystroff
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA. .,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA.
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60
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Kostaropoulos T, Papageorgiou L, Champeris Tsaniras S, Vlachakis D, Eliopoulos E. Carcinogenic Pesticide Control via Hijacking Endosymbiosis; The Paradigm of DSB-A from Wolbachia pipientis for the Management of Otiorhynchus singularis. In Vivo 2018; 32:1051-1062. [PMID: 30150426 PMCID: PMC6199590 DOI: 10.21873/invivo.11346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND/AIM Pesticides have little, if any specificity, to the pathogen they target in most cases. Wide spectrum toxic chemicals are being used to remove pestcides and salvage crops and economies linked to agriculture. The burden on the environment, public health and economy is huge. Traditional pestcide control is based on administering heavy loads of highly toxic compounds and elements that essentially strip all life from the field. Those chemicals are a leading cause of increased cancer related deaths in countryside. Herein, the Trojan horse of endosymbiosis was used, in an effort to control pests using high specificity compounds in reduced quantities. MATERIALS AND METHODS Our pipeline has been applied on the case of Otiorhynchus singularis, which is a very widespread pest, whose impact is devastating on a repertoire of crops. To date, there is no specific pesticide nor agent to control it. The deployed strategy involves the inhibition of the key DSB-A enzyme of its endosymbiotic Wolbachia pipientis bacterial strain. RESULTS Our methodology, provides the means to design, test and identify highly specific pestcide control substances that minimize the impact of toxic chemicals on health, economy and the environment. CONCLUSION All in all, in this study a radical computer-based pipeline is proposed that could be adopted under many other similar scenarios and pave the way for precision agriculture via optimized pest control.
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Affiliation(s)
- Thomas Kostaropoulos
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Louis Papageorgiou
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | - Dimitrios Vlachakis
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Faculty of Natural & Mathematical Sciences, King's College London, London, U.K
| | - Elias Eliopoulos
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
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61
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Ho CM, Beck JR, Lai M, Cui Y, Goldberg DE, Egea PF, Zhou ZH. Malaria parasite translocon structure and mechanism of effector export. Nature 2018; 561:70-75. [PMID: 30150771 PMCID: PMC6555636 DOI: 10.1038/s41586-018-0469-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022]
Abstract
The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the mechanism of this process remains unknown. Here we show that PTEX is a bona fide translocon by determining structures of the PTEX core complex at near-atomic resolution using cryo-electron microscopy. We isolated the endogenous PTEX core complex containing EXP2, PTEX150 and HSP101 from Plasmodium falciparum in the 'engaged' and 'resetting' states of endogenous cargo translocation using epitope tags inserted using the CRISPR-Cas9 system. In the structures, EXP2 and PTEX150 interdigitate to form a static, funnel-shaped pseudo-seven-fold-symmetric protein-conducting channel spanning the vacuolar membrane. The spiral-shaped AAA+ HSP101 hexamer is tethered above this funnel, and undergoes pronounced compaction that allows three of six tyrosine-bearing pore loops lining the HSP101 channel to dissociate from the cargo, resetting the translocon for the next threading cycle. Our work reveals the mechanism of P. falciparum effector export, and will inform structure-based design of drugs targeting this unique translocon.
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Affiliation(s)
- Chi-Min Ho
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Josh R Beck
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Mason Lai
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Daniel E Goldberg
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Pascal F Egea
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Z Hong Zhou
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.
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62
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High-throughput and scalable protein function identification with Hadoop and Map-only pattern of the MapReduce processing model. Knowl Inf Syst 2018. [DOI: 10.1007/s10115-018-1245-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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63
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Jin T, Brefo-Mensah E, Fan W, Zeng W, Li Y, Zhang Y, Palmer M. Crystal structure of the Streptococcus agalactiae CAMP factor provides insights into its membrane-permeabilizing activity. J Biol Chem 2018; 293:11867-11877. [PMID: 29884770 DOI: 10.1074/jbc.ra118.002336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/30/2018] [Indexed: 11/06/2022] Open
Abstract
Streptococcus agalactiae is an important human opportunistic pathogen that can cause serious health problems, particularly among newborns and older individuals. S. agalactiae contains the CAMP factor, a pore-forming toxin first identified in this bacterium. The CAMP reaction is based on the co-hemolytic activity of the CAMP factor and is commonly used to identify S. agalactiae in the clinic. Closely related proteins are present also in other Gram-positive pathogens. Although the CAMP toxin was discovered more than a half century ago, no structure from this toxin family has been reported, and the mechanism of action of this toxin remains unclear. Here, we report the first structure of this toxin family, revealing a structural fold composed of 5 + 3-helix bundles. Further analysis by protein truncation and site-directed mutagenesis indicated that the N-terminal 5-helix bundle is responsible for membrane permeabilization, whereas the C-terminal 3-helix bundle is likely responsible for host receptor binding. Interestingly, the C-terminal domain inhibited the activity of both full-length toxin and its N-terminal domain. Moreover, we observed that the linker region is highly conserved and has a conserved DLXXXDXAT sequence motif. Structurally, this linker region extensively interacted with both terminal CAMP factor domains, and mutagenesis disclosed that the conserved sequence motif is required for CAMP factor's co-hemolytic activity. In conclusion, our results reveal a unique structure of this bacterial toxin and help clarify the molecular mechanism of its co-hemolytic activity.
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Affiliation(s)
- Tengchuan Jin
- From the Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China,
| | - Eric Brefo-Mensah
- the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Weirong Fan
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai 201400, China, and
| | - Weihong Zeng
- From the Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yajuan Li
- From the Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yuzhu Zhang
- the Healthy Processed Foods Research Unit, United States Department of Agriculture Agricultural Research Service, Western Regional Research Center, Albany, California 94706
| | - Michael Palmer
- the Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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64
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Raboanatahiry N, Wang B, Yu L, Li M. Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops. Front Genet 2018; 9:182. [PMID: 29872448 PMCID: PMC5972291 DOI: 10.3389/fgene.2018.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022] Open
Abstract
Diversities in structure and function of ACBP were discussed in this review. ACBP are important proteins that could transport newly synthesized fatty acid, activated into -coA, from plastid to endoplasmic reticulum, where oil in the form of triacylglycerol occurs. ACBP were detected in various animal and plants species, which indicated their importance in biological function. In fact, involvement of ACBP in important process such as lipid metabolism, regulation of enzyme and gene expression, and in response to plant stresses has been proven in several studies. In this review, findings on ACBP of 11 well-known oil crops were reviewed to comprehend diversity, comparative analyses on ACBP structure were made, and link between structure and function, tissue expression and subcellular location of ACBP were also observed. Incomplete reports in some species were mentioned, which might be encouraging to start or to perform deeper studies. Similar characteristics were found in paralogs ACBP, and orthologs ACBP had different functions, despite the high identity in amino acid sequence. At the end, it is confirmed that ortholog proteins could not necessarily display the same function, even from closely related species.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
| | - Baoshan Wang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China
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65
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Leinweber M, Fober T, Freisleben B. GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:740-752. [PMID: 27845672 DOI: 10.1109/tcbb.2016.2625793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations. Binary classification tests based on the ATP, NADH, and FAD protein subsets of CavBase, a database containing putative binding sites, show average classification rate improvements from about 92 percent (CPU) to 96 percent (GPU). Further experiments indicate that the proposed GPU-based labeled point cloud superpositioning approach can be superior to traditional protein comparison approaches based on sequence alignments.
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Shen K, Huang RK, Brignole EJ, Condon KJ, Valenstein ML, Chantranupong L, Bomaliyamu A, Choe A, Hong C, Yu Z, Sabatini DM. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Nature 2018; 556:64-69. [PMID: 29590090 PMCID: PMC5975964 DOI: 10.1038/nature26158] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.
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Affiliation(s)
- Kuang Shen
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rick K. Huang
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Edward J. Brignole
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kendall J. Condon
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Max L. Valenstein
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aimaiti Bomaliyamu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Abigail Choe
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Chuan Hong
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David M. Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
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Rout RK, Pal Choudhury P, Maity SP, Daya Sagar BS, Hassan SS. Fractal and mathematical morphology in intricate comparison between tertiary protein structures. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING: IMAGING & VISUALIZATION 2018. [DOI: 10.1080/21681163.2016.1214850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ranjeet Kumar Rout
- Department of Computer Science and Engineering, National Institute of Technology, Jalandhar, India
| | | | - Santi Prasad Maity
- Information Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, India
| | - B. S. Daya Sagar
- Systems Science and Informatics Unit, Indian Statistical Institute (ISI), Bangalore, India
| | - Sk. Sarif Hassan
- Department of Mathematics, College of Engineering Studies, University of Petroleum and Energy Studies, Dehradun, India
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Structural and functional modeling of viral protein 5 of Infectious Bursal Disease Virus. Virus Res 2018; 247:55-60. [PMID: 29427596 DOI: 10.1016/j.virusres.2018.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 11/22/2022]
Abstract
Infectious Bursal Disease (IBD) is an acute, highly contagious and immunosuppressive disease of young chicken. The causative virus (IBDV) is a bi-segmented, double-stranded RNA virus. The virus encodes five major proteins, viral protein (VP) 1-5. VPs 1-3 have been characterized crystallographically. Albeit a rise in the number of studies reporting successful heterologous expression of VP5 in recent times, challenging the notion that rapid death of host cells overexpressing VP5 disallows obtaining sufficiently pure preparations of the protein for crystallographic studies, the structure of VP5 remains unknown and its function controversial. Our study describes the first 3D model of IBD VP5 obtained through an elaborate computational workflow. Based on the results of the study, IBD VP5 can be predicted to be a structural analog of the leucine-rich repeat (LRR) family of proteins. Functional implications arising from structural similarity of VP5 with host Toll-like receptor (Tlr) 3 also satisfy the previously reported opposing roles of the protein in first abolishing and later inducing host-cell apoptosis.
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Abstract
The significant expansion in protein sequence and structure data that we are now witnessing brings with it a pressing need to bring order to the protein world. Such order enables us to gain insights into the evolution of proteins, their function and the extent to which the functional repertoire can vary across the three kingdoms of life. This has lead to the creation of a wide range of protein family classifications that aim to group proteins based upon their evolutionary relationships.In this chapter we discuss the approaches and methods that are frequently used in the classification of proteins, with a specific emphasis on the classification of protein domains. The construction of both domain sequence and domain structure databases is considered and we show how the use of domain family annotations to assign structural and functional information is enhancing our understanding of genomes.
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70
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Ha BH, Boggon TJ. The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization. J Biol Chem 2017; 293:1642-1650. [PMID: 29212708 DOI: 10.1074/jbc.ra117.000751] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/30/2017] [Indexed: 01/18/2023] Open
Abstract
The pseudokinase group encompasses some 10% of protein kinases, but pseudokinases diverge from canonical kinases in key motifs. The two members of the small new kinase family 3 (NKF3) group are considered pseudokinases. These proteins, pseudopodium-enriched atypical kinase 1 (PEAK1, Sugen kinase 269, or SgK269) and pragmin (Sugen kinase 223 or SgK223), act as scaffolds in growth factor signaling pathways, and both contain a kinase fold with degraded kinase motifs at their C termini. These kinases may harbor regions that mediate oligomerization or control other aspects of signal transduction, but a lack of structural information has precluded detailed investigations into their functional roles. In this study, we determined the X-ray crystal structure of the PEAK1 pseudokinase domain to 2.3 Å resolution. The structure revealed that the PEAK1 kinase-like domain contains a closed nucleotide-binding cleft that in this conformation may deleteriously affect nucleotide binding. Moreover, we found that N- and C-terminal extensions create a highly unusual all α-helical split-dimerization region, termed here the split helical dimerization (SHED) region. Sequence conservation analysis suggested that this region facilitates a dimerization mode that is conserved between PEAK1 and pragmin. Finally, we observed structural similarities between the PEAK1 SHED region and the C-terminal extension of the Parkinson's disease-associated kinase PINK1. In summary, PEAK1's kinase cleft is occluded, and its newly identified SHED region may promote an unexpected dimerization mode. Similarities of PEAK1 with the active kinase PINK1 may reclassify the latter as a member of the new kinase family 3 group.
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Affiliation(s)
| | - Titus J Boggon
- From the Departments of Pharmacology and .,Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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71
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Ejlali N, Faghihi MR, Sadeghi M. Bayesian comparison of protein structures using partial Procrustes distance. Stat Appl Genet Mol Biol 2017; 16:243-257. [PMID: 28862992 DOI: 10.1515/sagmb-2016-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.
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72
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Engin HB, Carlin D, Pratt D, Carter H. Modeling of RAS complexes supports roles in cancer for less studied partners. BMC BIOPHYSICS 2017; 10:5. [PMID: 28815022 PMCID: PMC5558186 DOI: 10.1186/s13628-017-0037-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions. Results To address this question we constructed a RAS isoform-specific protein-protein interaction network and predicted 3D complexes involving RAS isoforms and interaction partners to identify the most probable interaction interfaces. The resulting models correctly captured the binding interfaces for well-studied effectors, and additionally implicated residues in the allosteric and hyper-variable regions of RAS proteins as the predominant binding site for non-canonical effectors. Several partners binding to this new interface (SRC, LGALS1, RABGEF1, CALM and RARRES3) have been implicated as important regulators of oncogenic RAS signaling. We further used these models to investigate competitive binding and multi-protein complexes compatible with RAS surface occupancy and the putative effects of somatic mutations on RAS protein interactions. Conclusions We discuss our findings in the context of RAS localization to the plasma membrane versus within the cytoplasm and provide a list of RAS protein interactions with possible cancer-related consequences, which could help guide future therapeutic strategies to target RAS proteins. Electronic supplementary material The online version of this article (doi:10.1186/s13628-017-0037-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H Billur Engin
- Division of Medical Genetics, Department of Medicine, Universsity of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093 USA
| | - Daniel Carlin
- Division of Medical Genetics, Department of Medicine, Universsity of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093 USA
| | - Dexter Pratt
- Division of Medical Genetics, Department of Medicine, Universsity of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093 USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, Universsity of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093 USA
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73
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Aggarwal A, Parai MK, Shetty N, Wallis D, Woolhiser L, Hastings C, Dutta NK, Galaviz S, Dhakal RC, Shrestha R, Wakabayashi S, Walpole C, Matthews D, Floyd D, Scullion P, Riley J, Epemolu O, Norval S, Snavely T, Robertson GT, Rubin EJ, Ioerger TR, Sirgel FA, van der Merwe R, van Helden PD, Keller P, Böttger EC, Karakousis PC, Lenaerts AJ, Sacchettini JC. Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13. Cell 2017; 170:249-259.e25. [PMID: 28669536 PMCID: PMC5509550 DOI: 10.1016/j.cell.2017.06.025] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/03/2017] [Accepted: 06/15/2017] [Indexed: 12/01/2022]
Abstract
Widespread resistance to first-line TB drugs is a major problem that will likely only be resolved through the development of new drugs with novel mechanisms of action. We have used structure-guided methods to develop a lead molecule that targets the thioesterase activity of polyketide synthase Pks13, an essential enzyme that forms mycolic acids, required for the cell wall of Mycobacterium tuberculosis. Our lead, TAM16, is a benzofuran class inhibitor of Pks13 with highly potent in vitro bactericidal activity against drug-susceptible and drug-resistant clinical isolates of M. tuberculosis. In multiple mouse models of TB infection, TAM16 showed in vivo efficacy equal to the first-line TB drug isoniazid, both as a monotherapy and in combination therapy with rifampicin. TAM16 has excellent pharmacological and safety profiles, and the frequency of resistance for TAM16 is ∼100-fold lower than INH, suggesting that it can be developed as a new antitubercular aimed at the acute infection. PAPERCLIP.
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Affiliation(s)
- Anup Aggarwal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Maloy K Parai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Nishant Shetty
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Deeann Wallis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Lisa Woolhiser
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Courtney Hastings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Noton K Dutta
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stacy Galaviz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ramesh C Dhakal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Rupesh Shrestha
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Shoko Wakabayashi
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Chris Walpole
- Structure-guided Drug Discovery Coalition, SGC Toronto, ON, Canada
| | - David Matthews
- Structure-guided Drug Discovery Coalition, SGC Toronto, ON, Canada
| | - David Floyd
- Structure-guided Drug Discovery Coalition, SGC Toronto, ON, Canada
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Suzanne Norval
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas Snavely
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Gregory T Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Frik A Sirgel
- NRF Centre of Excellence for Biomedical TB Research and the South African MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Ruben van der Merwe
- NRF Centre of Excellence for Biomedical TB Research and the South African MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Paul D van Helden
- NRF Centre of Excellence for Biomedical TB Research and the South African MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Peter Keller
- Institute of Medical Microbiology, National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Petros C Karakousis
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne J Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
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Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell 2017; 169:47-57.e11. [PMID: 28340349 DOI: 10.1016/j.cell.2017.03.012] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Abstract
Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3.4 Å. The structure explains the molecular mechanism for immune system suppression, and structure-guided mutations show that the Acr proteins bind to residues essential for crRNA-mediated detection of DNA. Collectively, these data provide a snapshot of an ongoing molecular arms race between viral suppressors and the immune system they target.
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Affiliation(s)
- Saikat Chowdhury
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Carter
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - MaryClare F Rollins
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Sarah M Golden
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Ryan N Jackson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Connor Hoffmann
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Lyn'Al Nosaka
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Elizabeth R Fischer
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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Hall CL, Lytle BL, Jensen D, Hoff JS, Peterson FC, Volkman BF, Kristich CJ. Structure and Dimerization of IreB, a Negative Regulator of Cephalosporin Resistance in Enterococcus faecalis. J Mol Biol 2017; 429:2324-2336. [PMID: 28551334 DOI: 10.1016/j.jmb.2017.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/05/2017] [Accepted: 05/18/2017] [Indexed: 11/30/2022]
Abstract
Enterococcus faecalis, a leading cause of hospital-acquired infections, exhibits intrinsic resistance to most cephalosporins, which are antibiotics in the beta-lactam family that target cell-wall biosynthesis. A comprehensive understanding of the underlying genetic and biochemical mechanisms of cephalosporin resistance in E. faecalis is lacking. We previously determined that a transmembrane serine/threonine kinase (IreK) and its cognate phosphatase (IreP) reciprocally regulate cephalosporin resistance in E. faecalis, dependent on the kinase activity of IreK. Other than IreK itself, thus far the only known substrate for reversible phosphorylation by IreK and IreP is IreB, a small protein of unknown function that is well conserved in low-GC Gram-positive bacteria. We previously showed that IreB acts as a negative regulator of cephalosporin resistance in E. faecalis. However, the biochemical mechanism by which IreB modulates cephalosporin resistance remains unknown. As a next step toward an understanding of the mechanism by which IreB regulates resistance, we initiated a structure-function study on IreB. The NMR solution structure of IreB was determined, revealing that IreB adopts a unique fold and forms a dimer in vitro. Dimerization of IreB was confirmed in vivo. Substitutions at the dimer interface impaired IreB function and stability in vivo, indicating that dimerization is functionally important for the biological activity of IreB. Hence, these studies provide new insights into the structure and function of a widely conserved protein of unknown function that is an important regulator of antimicrobial resistance in E. faecalis.
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Affiliation(s)
- Cherisse L Hall
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Betsy L Lytle
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Davin Jensen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jessica S Hoff
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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76
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Halabi S, Sekine E, Verstak B, Gay NJ, Moncrieffe MC. Structure of the Toll/Interleukin-1 Receptor (TIR) Domain of the B-cell Adaptor That Links Phosphoinositide Metabolism with the Negative Regulation of the Toll-like Receptor (TLR) Signalosome. J Biol Chem 2017; 292:652-660. [PMID: 27909057 PMCID: PMC5241739 DOI: 10.1074/jbc.m116.761528] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/15/2016] [Indexed: 02/02/2023] Open
Abstract
Ligand binding to Toll-like receptors (TLRs) results in dimerization of their cytosolic Toll/interleukin-1 receptor (TIR) domains and recruitment of post-receptor signal transducers into a complex signalosome. TLR activation leads to the production of transcription factors and pro-inflammatory molecules and the activation of phosphoinositide 3-kinases (PI3K) in a process that requires the multimodular B-cell adaptor for phosphoinositide 3-kinase (BCAP). BCAP has a sequence previously proposed as a "cryptic" TIR domain. Here, we present the structure of the N-terminal region of human BCAP and show that it possesses a canonical TIR fold. Dimeric BCAP associates with the TIR domains of TLR2/4 and MAL/TIRAP, suggesting that it is recruited to the TLR signalosome by multitypic TIR-TIR interactions. BCAP also interacts with the p85 subunit of PI3K and phospholipase Cγ, enzymes that deplete plasma membrane phosphatidylinositol 4,5-bisphosphate (PIP2), and these interactions provide a molecular explanation for BCAP-mediated down-regulation of inflammatory signaling.
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Affiliation(s)
- Samer Halabi
- From the Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom
| | - Eiki Sekine
- From the Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom
| | - Brett Verstak
- From the Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom
| | - Nicholas J. Gay
- From the Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom, To whom correspondence may be addressed: Dept. of Biochemistry, Cambridge University, Sanger Bldg., 80 Tennis Court Rd., Cambridge CB2 1GA, UK. Tel.: 44-1223-333-626; E-mail:
| | - Martin C. Moncrieffe
- From the Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom, To whom correspondence may be addressed: Dept. of Biochemistry, Cambridge University, Sanger Bldg., 80 Tennis Court Rd., Cambridge CB2 1GA, UK. Tel.: 44-1223-333-626; E-mail:
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Abstract
Protein function is a concept that can have different interpretations in different biological contexts, and the number and diversity of novel proteins identified by large-scale "omics" technologies poses increasingly new challenges. In this review we explore current strategies used to predict protein function focused on high-throughput sequence analysis, as for example, inference based on sequence similarity, sequence composition, structure, and protein-protein interaction. Various prediction strategies are discussed together with illustrative workflows highlighting the use of some benchmark tools and knowledge bases in the field.
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Affiliation(s)
- Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
| | - Sheyla Trefflich
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Vinícius Almir Weiss
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Mauro Antônio Alves Castro
- Sector of Professional and Technological Education, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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78
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Saxton RA, Chantranupong L, Knockenhauer KE, Schwartz TU, Sabatini DM. Mechanism of arginine sensing by CASTOR1 upstream of mTORC1. Nature 2016; 536:229-33. [PMID: 27487210 PMCID: PMC4988899 DOI: 10.1038/nature19079] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
The mechanistic Target of Rapamycin Complex 1 (mTORC1) is a major regulator of eukaryotic growth that coordinates anabolic and catabolic cellular processes with inputs such as growth factors and nutrients, including amino acids. In mammals arginine is particularly important, promoting diverse physiological effects such as immune cell activation, insulin secretion, and muscle growth, largely mediated through activation of mTORC1 (refs 4, 5, 6, 7). Arginine activates mTORC1 upstream of the Rag family of GTPases, through either the lysosomal amino acid transporter SLC38A9 or the GATOR2-interacting Cellular Arginine Sensor for mTORC1 (CASTOR1). However, the mechanism by which the mTORC1 pathway detects and transmits this arginine signal has been elusive. Here, we present the 1.8 Å crystal structure of arginine-bound CASTOR1. Homodimeric CASTOR1 binds arginine at the interface of two Aspartate kinase, Chorismate mutase, TyrA (ACT) domains, enabling allosteric control of the adjacent GATOR2-binding site to trigger dissociation from GATOR2 and downstream activation of mTORC1. Our data reveal that CASTOR1 shares substantial structural homology with the lysine-binding regulatory domain of prokaryotic aspartate kinases, suggesting that the mTORC1 pathway exploited an ancient, amino-acid-dependent allosteric mechanism to acquire arginine sensitivity. Together, these results establish a structural basis for arginine sensing by the mTORC1 pathway and provide insights into the evolution of a mammalian nutrient sensor.
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Affiliation(s)
- Robert A. Saxton
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Lynne Chantranupong
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
| | - Kevin E. Knockenhauer
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Thomas U. Schwartz
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - David M. Sabatini
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge MA 02142, USA
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79
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Talevi A. Computational approaches for innovative antiepileptic drug discovery. Expert Opin Drug Discov 2016; 11:1001-16. [DOI: 10.1080/17460441.2016.1216965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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80
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Saadhali SA, Hassan S, Hanna LE, Ranganathan UD, Kumar V. Homology modeling, substrate docking, and molecular simulation studies of mycobacteriophage Che12 lysin A. J Mol Model 2016; 22:180. [PMID: 27411553 DOI: 10.1007/s00894-016-3056-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/28/2016] [Indexed: 11/26/2022]
Abstract
Mycobacteriophages produce lysins that break down the host cell wall at the end of lytic cycle to release their progenies. The ability to lyse mycobacterial cells makes the lysins significant. Mycobacteriophage Che12 is the first reported temperate phage capable of infecting and lysogenising Mycobacterium tuberculosis. Gp11 of Che12 was found to have Chitinase domain that serves as endolysin (lysin A) for Che12. Structure of gp11 was modeled and evaluated using Ramachandran plot in which 98 % of the residues are in the favored and allowed regions. Che12 lysin A was predicted to act on NAG-NAM-NAG molecules in the peptidoglycan of cell wall. The tautomers of NAG-NAM-NAG molecule were generated and docked with lysin A. The stability and binding affinity of lysin A - NAG-NAM-NAG tautomers were studied using molecular dynamics simulations.
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Affiliation(s)
- Shainaba A Saadhali
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India
| | - Sameer Hassan
- Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Luke Elizabeth Hanna
- Department of Clinical Research, National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Uma Devi Ranganathan
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India
| | - Vanaja Kumar
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India.
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81
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HDInsight4PSi: Boosting performance of 3D protein structure similarity searching with HDInsight clusters in Microsoft Azure cloud. Inf Sci (N Y) 2016. [DOI: 10.1016/j.ins.2016.02.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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82
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Aslam N, Nadeem A, Babar ME, Pervez MT, Aslam M, Naveed N, Hussain T, Shehzad W, Wasim M, Bao Z, Javed M. The accuracy of protein structure alignment servers. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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83
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Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity. J Struct Biol 2016; 194:18-28. [PMID: 26796657 DOI: 10.1016/j.jsb.2016.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 01/13/2023]
Abstract
Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.
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84
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Reaching optimized parameter set: protein secondary structure prediction using neural network. Neural Comput Appl 2016. [DOI: 10.1007/s00521-015-2150-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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85
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Shivashankar N, Patil S, Bhosle A, Chandra N, Natarajan V. MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. BMC Bioinformatics 2016; 17:26. [PMID: 26753741 PMCID: PMC4710026 DOI: 10.1186/s12859-015-0874-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Background Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0874-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nithin Shivashankar
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India.
| | - Sonali Patil
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore, 560012, India
| | - Amrisha Bhosle
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Vijay Natarajan
- Department of Computer Science and Automation, and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560012, India.
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86
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Gutiérrez FI, Rodriguez-Valenzuela F, Ibarra IL, Devos DP, Melo F. Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. BMC Bioinformatics 2016; 17:20. [PMID: 26732380 PMCID: PMC4702403 DOI: 10.1186/s12859-015-0866-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/21/2015] [Indexed: 12/01/2022] Open
Abstract
Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery. Results Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery. Conclusions The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0866-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fernando I Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Felipe Rodriguez-Valenzuela
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Ignacio L Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.,Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide, Sevilla, Spain
| | - Damien P Devos
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany. .,Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide, Sevilla, Spain.
| | - Francisco Melo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
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87
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Gandhimathi A, Ghosh P, Hariharaputran S, Mathew OK, Sowdhamini R. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. Nucleic Acids Res 2016; 44:D410-4. [PMID: 26553811 PMCID: PMC4702857 DOI: 10.1093/nar/gkv1205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/12/2022] Open
Abstract
Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/.
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Affiliation(s)
- Arumugam Gandhimathi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, Karnataka, India
| | - Pritha Ghosh
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, Karnataka, India
| | - Sridhar Hariharaputran
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, Karnataka, India Bharathidasan University, Palkalainagar, Tiruchirapalli 620024, Tamilnadu, India
| | - Oommen K Mathew
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, Karnataka, India SASTRA University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India
| | - R Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore 560065, Karnataka, India
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88
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Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2016; 44:D7-19. [PMID: 26615191 PMCID: PMC4702911 DOI: 10.1093/nar/gkv1290] [Citation(s) in RCA: 1029] [Impact Index Per Article: 128.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/25/2022] Open
Abstract
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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89
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M. Fialho A, Bernardes N, M Chakrabarty A. Exploring the anticancer potential of the bacterial protein azurin. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.3.292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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90
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Kumari A, Kanchan S, Sinha RP, Kesheri M. Applications of Bio-molecular Databases in Bioinformatics. MEDICAL IMAGING IN CLINICAL APPLICATIONS 2016. [DOI: 10.1007/978-3-319-33793-7_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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91
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The Importance of Drug Repurposing in the Field of Antiepileptic Drug Development. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2016. [DOI: 10.1007/978-1-4939-6355-3_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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92
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Saxton RA, Knockenhauer KE, Wolfson RL, Chantranupong L, Pacold ME, Wang T, Schwartz TU, Sabatini DM. Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway. Science 2015; 351:53-8. [PMID: 26586190 DOI: 10.1126/science.aad2087] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/05/2015] [Indexed: 12/12/2022]
Abstract
Eukaryotic cells coordinate growth with the availability of nutrients through the mechanistic target of rapamycin complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag guanosine triphosphatases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. Here we present the 2.7 angstrom crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucine leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. These results provide a structural mechanism of amino acid sensing by the mTORC1 pathway.
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Affiliation(s)
- Robert A Saxton
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kevin E Knockenhauer
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Rachel L Wolfson
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Lynne Chantranupong
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael E Pacold
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Tim Wang
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
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93
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Mezulis S, Sternberg MJE, Kelley LA. PhyreStorm: A Web Server for Fast Structural Searches Against the PDB. J Mol Biol 2015; 428:702-708. [PMID: 26517951 PMCID: PMC7610957 DOI: 10.1016/j.jmb.2015.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/13/2015] [Accepted: 10/18/2015] [Indexed: 11/10/2022]
Abstract
The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93 ± 2% of all highly similar (TM-score > 0.7) structures in the PDB for each query structure, usually in less than 60 s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/.
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Affiliation(s)
- Stefans Mezulis
- Structural Bioinformatics Group, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Michael J E Sternberg
- Structural Bioinformatics Group, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lawrence A Kelley
- Structural Bioinformatics Group, Imperial College London, London SW7 2AZ, United Kingdom
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94
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Waghu FH, Barai RS, Gurung P, Idicula-Thomas S. CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res 2015; 44:D1094-7. [PMID: 26467475 PMCID: PMC4702787 DOI: 10.1093/nar/gkv1051] [Citation(s) in RCA: 436] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial peptides (AMPs) are known to have family-specific sequence composition, which can be mined for discovery and design of AMPs. Here, we present CAMPR3; an update to the existing CAMP database available online at www.camp3.bicnirrh.res.in. It is a database of sequences, structures and family-specific signatures of prokaryotic and eukaryotic AMPs. Family-specific sequence signatures comprising of patterns and Hidden Markov Models were generated for 45 AMP families by analysing 1386 experimentally studied AMPs. These were further used to retrieve AMPs from online sequence databases. More than 4000 AMPs could be identified using these signatures. AMP family signatures provided in CAMPR3 can thus be used to accelerate and expand the discovery of AMPs. CAMPR3 presently holds 10247 sequences, 757 structures and 114 family-specific signatures of AMPs. Users can avail the sequence optimization algorithm for rational design of AMPs. The database integrated with tools for AMP sequence and structure analysis will be a valuable resource for family-based studies on AMPs.
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Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Pratima Gurung
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
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95
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Hudek L, Pearson L, Michalczyk AA, Bräu L, Neilan BA, Ackland ML. Characterization of two cation diffusion facilitators NpunF0707 and NpunF1794 in Nostoc punctiforme. J Appl Microbiol 2015; 119:1357-70. [PMID: 26299407 DOI: 10.1111/jam.12942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 11/28/2022]
Abstract
AIMS To characterize genes involved in maintaining homeostatic levels of zinc in the cyanobacterium Nostoc punctiforme. METHODS AND RESULTS Metal efflux transporters play a central role in maintaining homeostatic levels of trace elements such as zinc. Sequence analyses of the N. punctiforme genome identified two potential cation diffusion facilitator (CDF) metal efflux transporters, Npun_F0707 (Cdf31) and Npun_F1794 (Cdf33). Deletion of either Cdf31or Cdf33 resulted in increased zinc retention over 3 h. Interestingly, Cdf31(-) and Cdf33(-) mutants showed no change in sensitivity to zinc exposure in comparison with the wild type, suggesting some compensatory capacity for the loss of each other. Using qRT-PCR, a possible interaction was observed between the two cdf's, where the Cdf31(-) mutant had a more profound effect on cdf33 expression than Cdf33(-) did on cdf31. Over-expression of Cdf31 and Cdf33 in ZntA(-) - and ZitB(-) -deficient Escherichia coli revealed function similarities between the ZntA and ZitB of E. coli and the cyanobacterial transporters. CONCLUSIONS The data presented shed light on the function of two important transporters that regulate zinc homeostasis in N. punctiforme. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows for the first time the functional characterization of two cyanobacterial zinc efflux proteins belonging to the CDF family.
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Affiliation(s)
- L Hudek
- Centre for Regional and Rural Futures, Deakin University, Burwood, Melbourne, Vic., Australia.,Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Vic., Australia
| | - L Pearson
- Australian Centre for Astrobiology and School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW, Australia
| | - A A Michalczyk
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Vic., Australia
| | - L Bräu
- Centre for Regional and Rural Futures, Deakin University, Burwood, Melbourne, Vic., Australia.,Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Vic., Australia
| | - B A Neilan
- Australian Centre for Astrobiology and School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW, Australia
| | - M L Ackland
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, Vic., Australia
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96
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Bikash T, Chandra JS, Premchand M, Samrat A. Functional and catalytic active sites prediction and docking analysis of azoreductase enzyme in Pseudomonas putida with a variety of commercially available azodyes. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajb2015.14699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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97
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Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophys J 2015. [PMID: 26213149 DOI: 10.1016/j.bpj.2015.06.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank; however, available protein complexes cover less than 10% of the human proteome. Although it is theoretically possible to infer interactions in human proteins based on structures of homologous protein complexes, it is still unclear to what extent protein interactions and binding sites are conserved, and whether protein complexes from remotely related species can be used to infer interactions and binding sites. We considered biological units of protein complexes and clustered protein-protein binding sites into similarity groups based on their structure and sequence, which allowed us to identify unique binding sites. We showed that the growth rate of the number of unique binding sites in the Protein Data Bank was much slower than the growth rate of the number of structural complexes. Next, we investigated the evolutionary roots of unique binding sites and identified the major phyletic branches with the largest expansion in the number of novel binding sites. We found that many binding sites could be traced to the universal common ancestor of all cellular organisms, whereas relatively few binding sites emerged at the major evolutionary branching points. We analyzed the physicochemical properties of unique binding sites and found that the most ancient sites were the largest in size, involved many salt bridges, and were the most compact and least planar. In contrast, binding sites that appeared more recently in the evolution of eukaryotes were characterized by a larger fraction of polar and aromatic residues, and were less compact and more planar, possibly due to their more transient nature and roles in signaling processes.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Alexey K Shaytan
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Benjamin A Shoemaker
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland
| | - Anna R Panchenko
- Computational Biology Branch of the National Center for Biotechnology Information, Bethesda, Maryland.
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98
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Structure of a herpesvirus nuclear egress complex subunit reveals an interaction groove that is essential for viral replication. Proc Natl Acad Sci U S A 2015; 112:9010-5. [PMID: 26150520 DOI: 10.1073/pnas.1511140112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Herpesviruses require a nuclear egress complex (NEC) for efficient transit of nucleocapsids from the nucleus to the cytoplasm. The NEC orchestrates multiple steps during herpesvirus nuclear egress, including disruption of nuclear lamina and particle budding through the inner nuclear membrane. In the important human pathogen human cytomegalovirus (HCMV), this complex consists of nuclear membrane protein UL50, and nucleoplasmic protein UL53, which is recruited to the nuclear membrane through its interaction with UL50. Here, we present an NMR-determined solution-state structure of the murine CMV homolog of UL50 (M50; residues 1-168) with a strikingly intricate protein fold that is matched by no other known protein folds in its entirety. Using NMR methods, we mapped the interaction of M50 with a highly conserved UL53-derived peptide, corresponding to a segment that is required for heterodimerization. The UL53 peptide binding site mapped onto an M50 surface groove, which harbors a large cavity. Point mutations of UL50 residues corresponding to surface residues in the characterized M50 heterodimerization interface substantially decreased UL50-UL53 binding in vitro, eliminated UL50-UL53 colocalization, prevented disruption of nuclear lamina, and halted productive virus replication in HCMV-infected cells. Our results provide detailed structural information on a key protein-protein interaction involved in nuclear egress and suggest that NEC subunit interactions can be an attractive drug target.
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99
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Gray C, Price CW, Lee CT, Dewald AH, Cline MA, McAnany CE, Columbus L, Mura C. Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 43:245-62. [PMID: 26148241 PMCID: PMC4758391 DOI: 10.1002/bmb.20873] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/14/2015] [Indexed: 05/27/2023]
Abstract
Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry- and research-based could simultaneously impart scientific knowledge and foster a student's research expertise and confidence. We have developed a year-long undergraduate biochemistry laboratory curriculum wherein students determine, via experiment and computation, the function of a protein of known three-dimensional structure. The first half of the course is inquiry-based and modular in design; students learn general biochemical techniques while gaining preparation for research experiments in the second semester. Having learned standard biochemical methods in the first semester, students independently pursue their own (original) research projects in the second semester. This new curriculum has yielded an improvement in student performance and confidence as assessed by various metrics. To disseminate teaching resources to students and instructors alike, a freely accessible Biochemistry Laboratory Education resource is available at http://biochemlab.org.
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Affiliation(s)
- Cynthia Gray
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Carol W Price
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Christopher T Lee
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Alison H Dewald
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Matthew A Cline
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Charles E McAnany
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22904
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100
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Raboanatahiry NH, Lu G, Li M. Computational Prediction of acyl-coA Binding Proteins Structure in Brassica napus. PLoS One 2015; 10:e0129650. [PMID: 26065422 PMCID: PMC4465970 DOI: 10.1371/journal.pone.0129650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/11/2015] [Indexed: 11/18/2022] Open
Abstract
Acyl-coA binding proteins could transport acyl-coA esters from plastid to endoplasmic reticulum, prior to fatty acid biosynthesis, leading to the formation of triacylglycerol. The structure and the subcellular localization of acyl-coA binding proteins (ACBP) in Brassica napus were computationally predicted in this study. Earlier, the structure analysis of ACBPs was limited to the small ACBPs, the current study focused on all four classes of ACBPs. Physicochemical parameters including the size and the length, the intron-exon structure, the isoelectric point, the hydrophobicity, and the amino acid composition were studied. Furthermore, identification of conserved residues and conserved domains were carried out. Secondary structure and tertiary structure of ACBPs were also studied. Finally, subcellular localization of ACBPs was predicted. The findings indicated that the physicochemical parameters and subcellular localizations of ACBPs in Brassica napus were identical to Arabidopsis thaliana. Conserved domain analysis indicated that ACBPs contain two or three kelch domains that belong to different families. Identical residues in acyl-coA binding domains corresponded to eight amino acid residues in all ACBPs of B. napus. However, conserved residues of common ACBPs in all species of animal, plant, bacteria and fungi were only inclusive in small ACBPs. Alpha-helixes were displayed and conserved in all the acyl-coA binding domains, representing almost the half of the protein structure. The findings confirm high similarities in ACBPs between A. thaliana and B. napus, they might share the same functions but loss or gain might be possible.
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Affiliation(s)
- Nadia Haingotiana Raboanatahiry
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, 435599, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, 430062, China
- * E-mail: (GL); (ML)
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, 435599, China
- * E-mail: (GL); (ML)
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