101
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Liu N, Fosses A, Kampik C, Parsiegla G, Denis Y, Vita N, Fierobe HP, Perret S. In vitro and in vivo exploration of the cellobiose and cellodextrin phosphorylases panel in Ruminiclostridium cellulolyticum: implication for cellulose catabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:208. [PMID: 31497068 PMCID: PMC6720390 DOI: 10.1186/s13068-019-1549-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/24/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND In anaerobic cellulolytic micro-organisms, cellulolysis results in the action of several cellulases gathered in extracellular multi-enzyme complexes called cellulosomes. Their action releases cellobiose and longer cellodextrins which are imported and further degraded in the cytosol to fuel the cells. In Ruminiclostridium cellulolyticum, an anaerobic and cellulolytic mesophilic bacteria, three cellodextrin phosphorylases named CdpA, CdpB, and CdpC, were identified in addition to the cellobiose phosphorylase (CbpA) previously characterized. The present study aimed at characterizing them, exploring their implication during growth on cellulose to better understand the life-style of cellulolytic bacteria on such substrate. RESULTS The three cellodextrin phosphorylases from R. cellulolyticum displayed marked different enzymatic characteristics. They are specific for cellodextrins of different lengths and present different k cat values. CdpC is the most active enzyme before CdpA, and CdpB is weakly active. Modeling studies revealed that a mutation of a conserved histidine residue in the phosphate ion-binding pocket in CdpB and CdpC might explain their activity-level differences. The genes encoding these enzymes are scattered over the chromosome of R. cellulolyticum and only the expression of the gene encoding the cellobiose phosphorylase and the gene cdpA is induced during cellulose growth. Characterization of four independent mutants constructed in R. cellulolyticum for each of the cellobiose and cellodextrin phosphorylases encoding genes indicated that only the cellobiose phosphorylase is essential for growth on cellulose. CONCLUSIONS Unexpectedly, the cellobiose phosphorylase but not the cellodextrin phosphorylases is essential for the growth of the model bacterium on cellulose. This suggests that the bacterium adopts a "short" dextrin strategy to grow on cellulose, even though the use of long cellodextrins might be more energy-saving. Our results suggest marked differences in the cellulose catabolism developed among cellulolytic bacteria, which is a result that might impact the design of future engineered strains for biomass-to-biofuel conversion.
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Affiliation(s)
- Nian Liu
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Aurélie Fosses
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Clara Kampik
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | | | - Yann Denis
- Aix-Marseille Univ, CNRS, Plateforme Transcriptome, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Henri-Pierre Fierobe
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Stéphanie Perret
- Aix-Marseille Univ, CNRS, LCB UMR 7283, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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102
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Properties of a Non-canonical Complex Formed Between a Tepary Bean (Phaseolus acutifolius) Protease Inhibitor and α-Chymotrypsin. Protein J 2019; 38:435-446. [PMID: 31435809 DOI: 10.1007/s10930-019-09863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protease inhibitors are crucial for the control of proteolytic activity in different physiological processes. However, some inhibitors do not show canonical enzyme recognition of the enzyme under certain conditions. In this work, we present evidence that indicates the formation of an active complex between the protease bovine α-chymotrypsin and the Tepary bean protease inhibitor (TBPI). The composition of the active chymotrypsin-TBPI complex (AC) was confirmed by three different methods: size-exclusion chromatography, polyacrylamide gel electrophoresis (PAGE), and mass spectrometry. The kinetic parameters for the AC were similar to those of the enzyme alone, indicating that TBPI binding does not produce any large changes in chymotrypsin. The molecular model proposed here postulates that TBPI binds outside the active cleft of the protease, but near enough to hinder the binding of high molecular weight substrates into the active site. This model was experimentally supported by the inhibitory effect on casein as a substrate, and the unaltered protease activity when a small synthetic substrate was used. We also found that the formation of this complex provided the enzyme with extra stability in denaturing conditions or in the presence of a reducing agent. The chymotrypsin-TBPI complex exhibited higher stability, indicating that autolysis can be partially prevented. When the enzyme was first inactivated followed by the addition of the inhibitor, the activity of the protease was restored. We described a possible mechanism where a plant protease inhibitor binds outside the active site of the enzyme while increasing its stability.
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103
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Hasan M, Islam S, Chakraborty S, Mustafa AH, Azim KF, Joy ZF, Hossain MN, Foysal SH, Hasan MN. Contriving a chimeric polyvalent vaccine to prevent infections caused by herpes simplex virus (type-1 and type-2): an exploratory immunoinformatic approach. J Biomol Struct Dyn 2019; 38:2898-2915. [PMID: 31328668 DOI: 10.1080/07391102.2019.1647286] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) and 2 (HSV-2) cause a variety of infections including oral-facial infections, genital herpes, herpes keratitis, cutaneous infection and so on. To date, FDA-approved licensed HSV vaccine is not available yet. Hence, the study was conducted to identify and characterize an effective epitope based polyvalent vaccine against both types of Herpes Simplex Virus. The selected proteins were retrieved from ViralZone and assessed to design highly antigenic epitopes by binding analyses of the peptides with MHC class-I and class-II molecules, antigenicity screening, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach. The final vaccine was constructed by the combination of top CTL, HTL and BCL epitopes from each protein along with suitable adjuvant and linkers. Physicochemical and secondary structure analysis, disulfide engineering, molecular dynamic simulation and codon adaptation were further employed to develop a unique multi-epitope peptide vaccine. Docking analysis of the refined vaccine structure with different MHC molecules and human immune TLR-2 receptor demonstrated higher interaction. Complexed structure of the modeled vaccine and TLR-2 showed minimal deformability at molecular level. Moreover, translational potency and microbial expression of the modeled vaccine was analyzed with pET28a(+) vector for E. coli strain K12 and the vaccine constructs had no similarity with entire human proteome. The study enabled design of a novel chimeric polyvalent vaccine to confer broad range immunity against both HSV serotypes. However, further wet lab based research using model animals are highly recommended to experimentally validate our findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Shiful Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sourav Chakraborty
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abu Hasnat Mustafa
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ziaul Faruque Joy
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.,Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Shakhawat Hossain Foysal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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104
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Assembling multidomain protein structures through analogous global structural alignments. Proc Natl Acad Sci U S A 2019; 116:15930-15938. [PMID: 31341084 DOI: 10.1073/pnas.1905068116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Most proteins exist with multiple domains in cells for cooperative functionality. However, structural biology and protein folding methods are often optimized for single-domain structures, resulting in a rapidly growing gap between the improved capability for tertiary structure determination and high demand for multidomain structure models. We have developed a pipeline, termed DEMO, for constructing multidomain protein structures by docking-based domain assembly simulations, with interdomain orientations determined by the distance profiles from analogous templates as detected through domain-level structure alignments. The pipeline was tested on a comprehensive benchmark set of 356 proteins consisting of 2-7 continuous and discontinuous domains, for which DEMO generated models with correct global fold (TM-score > 0.5) for 86% of cases with continuous domains and for 100% of cases with discontinuous domain structures, starting from randomly oriented target-domain structures. DEMO was also applied to reassemble multidomain targets in the CASP12 and CASP13 experiments using domain structures excised from the top server predictions, where the full-length DEMO models showed a significantly improved quality over the original server models. Finally, sparse restraints of mass spectrometry-generated cross-linking data and cryo-EM density maps are incorporated into DEMO, resulting in improvements in the average TM-score by 6.3% and 12.5%, respectively. The results demonstrate an efficient approach to assembling multidomain structures, which can be easily used for automated, genome-scale multidomain protein structure assembly.
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105
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Dapkūnas J, Olechnovič K, Venclovas Č. Structural modeling of protein complexes: Current capabilities and challenges. Proteins 2019; 87:1222-1232. [PMID: 31294859 DOI: 10.1002/prot.25774] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/27/2022]
Abstract
Proteins frequently interact with each other, and the knowledge of structures of the corresponding protein complexes is necessary to understand how they function. Computational methods are increasingly used to provide structural models of protein complexes. Not surprisingly, community-wide Critical Assessment of protein Structure Prediction (CASP) experiments have recently started monitoring the progress in this research area. We participated in CASP13 with the aim to evaluate our current capabilities in modeling of protein complexes and to gain a better understanding of factors that exert the largest impact on these capabilities. To model protein complexes in CASP13, we applied template-based modeling, free docking and hybrid techniques that enabled us to generate models of the topmost quality for 27 of 42 multimers. If templates for protein complexes could be identified, we modeled the structures with reasonable accuracy by straightforward homology modeling. If only partial templates were available, it was nevertheless possible to predict the interaction interfaces correctly or to generate acceptable models for protein complexes by combining template-based modeling with docking. If no templates were available, we used rigid-body docking with limited success. However, in some free docking models, despite the incorrect subunit orientation and missed interface contacts, the approximate location of protein binding sites was identified correctly. Apparently, our overall performance in docking was limited by the quality of monomer models and by the imperfection of scoring methods. The impact of human intervention on our results in modeling of protein complexes was significant indicating the need for improvements of automatic methods.
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Affiliation(s)
- Justas Dapkūnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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106
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Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M. The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor. Nucleic Acids Res 2019; 46:2560-2572. [PMID: 29471489 PMCID: PMC5861437 DOI: 10.1093/nar/gky107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/08/2018] [Indexed: 11/13/2022] Open
Abstract
CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has unusual Walker A and Motif VI sequences those nonetheless have their expected functions. Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163–aa 172), that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a dimeric complex.
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Affiliation(s)
- Paulius Toliusis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rokas Grigaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Donata Tuminauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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107
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Li D, Wang J, Jin Z, Zhang Z. Structural and evolutionary characteristics of dynamin-related GTPase OPA1. PeerJ 2019; 7:e7285. [PMID: 31328044 PMCID: PMC6622160 DOI: 10.7717/peerj.7285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/12/2019] [Indexed: 12/29/2022] Open
Abstract
OPA1 is a dynamin-related GTPase that controls mitochondrial fusion, cristae remodeling, energetics and mtDNA maintenance. However, the molecular architecture of OPA1 is poorly understood. Here we modeled the structure of human OPA1 by the threading approach. We found that the C-terminal region of the OPA1 protein had multiple functional domains, while the N-terminal region was rich in alpha helices and did not include specific domains. For the short soluble forms of OPA1, we observed that there were obvious hydrophobic regions near the two cleavage sites and the N-terminal was positively charged after cleavage. The blue native analysis revealed that the protein could form stable homodimers. In addition, the evolutionary conservation of the C-terminal region, where most of the known mutated disease-related sites were located, was significantly higher than that of the N-terminal region. These findings provided new insights into the structure and biochemical function of OPA1.
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Affiliation(s)
- Dandan Li
- College of Biological Sciences, China Agricultural University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Jinlan Wang
- Physical Examination Office of Shandong Province, Health Commission of Shandong Province, Jinan, China
| | - Zichen Jin
- Department of Chemistry, University of Minnesota, Minnesota, MN, USA
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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108
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Wang D, Geng L, Zhao YJ, Yang Y, Huang Y, Zhang Y, Shen HB. Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics 2019; 36:437-448. [PMID: 31274151 PMCID: PMC7999140 DOI: 10.1093/bioinformatics/btz544] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/06/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Protein structure refinement is an important step of protein structure prediction. Existing approaches have generally used a single scoring function combined with Monte Carlo method or Molecular Dynamics algorithm. The one-dimension optimization of a single energy function may take the structure too far away without a constraint. The basic motivation of our study is to reduce the bias problem caused by minimizing only a single energy function due to the very diversity of different protein structures. RESULTS We report a new Artificial Intelligence-based protein structure Refinement method called AIR. Its fundamental idea is to use multiple energy functions as multi-objectives in an effort to correct the potential inaccuracy from a single function. A multi-objective particle swarm optimization algorithm-based structure refinement is designed, where each structure is considered as a particle in the protocol. With the refinement iterations, the particles move around. The quality of particles in each iteration is evaluated by three energy functions, and the non-dominated particles are put into a set called Pareto set. After enough iteration times, particles from the Pareto set are screened and part of the top solutions are outputted as the final refined structures. The multi-objective energy function optimization strategy designed in the AIR protocol provides a different constraint view of the structure, by extending the one-dimension optimization to a new three-dimension space optimization driven by the multi-objective particle swarm optimization engine. Experimental results on CASP11, CASP12 refinement targets and blind tests in CASP 13 turn to be promising. AVAILABILITY AND IMPLEMENTATION The AIR is available online at: www.csbio.sjtu.edu.cn/bioinf/AIR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Yu-Jun Zhao
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Huang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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109
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Azim KF, Hasan M, Hossain MN, Somana SR, Hoque SF, Bappy MNI, Chowdhury AT, Lasker T. Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus). INFECTION GENETICS AND EVOLUTION 2019; 74:103936. [PMID: 31233780 DOI: 10.1016/j.meegid.2019.103936] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
Abstract
Norovirus is known as a major cause of several acute gastroenteritis (AGE) outbreaks each year. A study was conducted to develop a unique multi epitope subunit vaccine against human norovirus by adopting reverse vaccinology approach. The entire viral proteome of Norwalk virus was retrieved and allowed for further in silico study to predict highly antigenic epitopes through antigenicity, transmembrane topology screening, allergenicity assessment, toxicity analysis, population coverage analysis and molecular docking approach. Capsid protein VP1 and protein VP2 were identified as most antigenic viral proteins which generated a plethora of antigenic epitopes. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, hydrophilicity, theoretical PI and structural behavior. Molecular docking analysis of the refined vaccine with different MHCs and human immune TLR8 receptor demonstrated higher binding interaction as well. Complexed structure of the modeled vaccine and TLR8 showed minimal deformability at molecular level. The designed construct was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for its heterologous cloning and expression, and sequence of vaccine constructs showed no similarity with human proteins. However, the study could initiate in vitro and in vivo studies regarding effective vaccine development against human norovirus.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Saneya Risa Somana
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Syeda Farjana Hoque
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Anjum Taiebah Chowdhury
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tahera Lasker
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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110
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Yu Z, Yao Y, Deng H, Yi M. ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment. BMC Bioinformatics 2019; 20:299. [PMID: 31159742 PMCID: PMC6547486 DOI: 10.1186/s12859-019-2898-y] [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: 11/28/2018] [Accepted: 05/13/2019] [Indexed: 01/05/2023] Open
Abstract
Background The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as decoy discrimination. However, these two aspects are found to be mutually exclusive in many statistical potentials. Results We developed an atomic ANgle- and DIStance-dependent (ANDIS) statistical potential for protein structure quality assessment with distance cutoff being a tunable parameter. When distance cutoff is ≤9.0 Å, “effective atomic interaction” is employed to enhance the ability of native recognition. For a distance cutoff of ≥10 Å, the distance-dependent atom-pair potential with random-walk reference state is combined to strengthen the ability of decoy discrimination. Benchmark tests on 632 structural decoy sets from diverse sources demonstrate that ANDIS outperforms other state-of-the-art potentials in both native recognition and decoy discrimination. Conclusions Distance cutoff is a crucial parameter for distance-dependent statistical potentials. A lower distance cutoff is better for native recognition, while a higher one is favorable for decoy discrimination. The ANDIS potential is freely available as a standalone application at http://qbp.hzau.edu.cn/ANDIS/. Electronic supplementary material The online version of this article (10.1186/s12859-019-2898-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhongwang Yu
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuangen Yao
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyou Deng
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China. .,Institute of Applied Physics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Ming Yi
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, 430070, China. .,Institute of Applied Physics, Huazhong Agricultural University, Wuhan, 430070, China.
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111
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Hasan M, Azim KF, Begum A, Khan NA, Shammi TS, Imran AS, Chowdhury IM, Urme SRA. Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus. INFECTION GENETICS AND EVOLUTION 2019; 70:140-157. [DOI: 10.1016/j.meegid.2019.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/09/2019] [Accepted: 03/04/2019] [Indexed: 12/23/2022]
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112
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Tang L, Yang J, Chen J, Zhang J, Yu H, Shen Z. Design of salt-bridge cyclization peptide tags for stability and activity enhancement of enzymes. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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113
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Khan GM, Hassan N, Khan N, Humayun M, Khan K, Khaliq S, Rehman FU, Ahmed S, Shah K, Khan SA, Muhammad N, Wali A, Khan S, Basit S, Ayub M. Biallelic mutations in the
LPAR
6
gene causing autosomal recessive wooly hair/hypotrichosis phenotype in five Pakistani families. Int J Dermatol 2019; 58:946-952. [DOI: 10.1111/ijd.14480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/25/2019] [Accepted: 04/11/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Ghulam M. Khan
- Institute of Biochemistry University of Balochistan Quetta Pakistan
| | - Noor Hassan
- Institute of Biochemistry University of Balochistan Quetta Pakistan
| | - Niamatullah Khan
- Department of Biotechnology & Genetic Engineering Kohat University of Science & Technology Kohat Khyber Pakhtunkhwa Pakistan
| | - Muhammad Humayun
- Department of Biotechnology & Genetic Engineering Kohat University of Science & Technology Kohat Khyber Pakhtunkhwa Pakistan
| | - Kafaitullah Khan
- Department of Microbiology University of Balochistan Quetta Pakistan
| | - Samira Khaliq
- Institute of Biochemistry University of Balochistan Quetta Pakistan
| | - Fazal U. Rehman
- Department of Microbiology University of Balochistan Quetta Pakistan
| | - Sheikh Ahmed
- Institute of Biochemistry University of Balochistan Quetta Pakistan
| | - Khadim Shah
- Department of Biotechnology COMSATS University Islamabad Abbottabad Campus Pakistan
| | - Sher A. Khan
- Department of Biotechnology & Genetic Engineering Kohat University of Science & Technology Kohat Khyber Pakhtunkhwa Pakistan
| | - Noor Muhammad
- Department of Biotechnology & Genetic Engineering Kohat University of Science & Technology Kohat Khyber Pakhtunkhwa Pakistan
| | - Abdul Wali
- Department of Biotechnology Faculty of Life Sciences & Informatics BUITEMS Quetta Pakistan
| | - Saadullah Khan
- Department of Biotechnology & Genetic Engineering Kohat University of Science & Technology Kohat Khyber Pakhtunkhwa Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases Taibah University Almadinah Almadinah Saudi Arabia
| | - Muhammad Ayub
- Institute of Biochemistry University of Balochistan Quetta Pakistan
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Methods for the Refinement of Protein Structure 3D Models. Int J Mol Sci 2019; 20:ijms20092301. [PMID: 31075942 PMCID: PMC6539982 DOI: 10.3390/ijms20092301] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 12/25/2022] Open
Abstract
The refinement of predicted 3D protein models is crucial in bringing them closer towards experimental accuracy for further computational studies. Refinement approaches can be divided into two main stages: The sampling and scoring stages. Sampling strategies, such as the popular Molecular Dynamics (MD)-based protocols, aim to generate improved 3D models. However, generating 3D models that are closer to the native structure than the initial model remains challenging, as structural deviations from the native basin can be encountered due to force-field inaccuracies. Therefore, different restraint strategies have been applied in order to avoid deviations away from the native structure. For example, the accurate prediction of local errors and/or contacts in the initial models can be used to guide restraints. MD-based protocols, using physics-based force fields and smart restraints, have made significant progress towards a more consistent refinement of 3D models. The scoring stage, including energy functions and Model Quality Assessment Programs (MQAPs) are also used to discriminate near-native conformations from non-native conformations. Nevertheless, there are often very small differences among generated 3D models in refinement pipelines, which makes model discrimination and selection problematic. For this reason, the identification of the most native-like conformations remains a major challenge.
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115
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Zhang P, Zhang Z, Li ZF, Chen Q, Li YY, Gong Y, Yue XJ, Sheng DH, Zhang YM, Wu C, Li YZ. Phylogeny-guided characterization of glycosyltransferases for epothilone glycosylation. Microb Biotechnol 2019; 12:763-774. [PMID: 31069998 PMCID: PMC6559208 DOI: 10.1111/1751-7915.13421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/05/2019] [Accepted: 04/16/2019] [Indexed: 12/03/2022] Open
Abstract
Glycosylation of natural products can influence their pharmacological properties, and efficient glycosyltransferases (GTs) are critical for this purpose. The polyketide epothilones are potent anti‐tumour compounds, and YjiC is the only reported GT for the glycosylation of epothilone. In this study, we phylogenetically analysed 8261 GTs deposited in CAZy database and revealed that YjiC locates in a subbranch of the Macrolide I group, forming the YjiC‐subbranch with 160 GT sequences. We demonstrated that the YjiC‐subbranch GTs are normally efficient in epothilone glycosylation, but some showed low glycosylation activities. Sequence alignment of YjiC‐subbranch showed that the 66th and 77th amino acid residues, which were close to the catalytic cavity in molecular docking model, were conserved in five high‐active GTs (Q66 and P77) but changed in two low‐efficient GTs. Site‐directed residues swapping at the two positions in the two low‐active GTs (BssGT and BamGT) and the high‐active GT BsGT‐1 demonstrated that the two amino acid residues played an important role in the catalytic efficiency of epothilone glycosylation. This study highlights that the potent GTs for appointed compounds are phylogenetically grouped with conserved residues for the catalytic efficiency.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhi-Feng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yao-Yao Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - You-Ming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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Sharma N, O'Neal AJ, Gonzalez C, Wittling M, Gjinaj E, Parsons LM, Panda D, Khalenkov A, Scott D, Misra S, Rabin RL. S27 of IFNα1 Contributes to Its Low Affinity for IFNAR2 and Weak Antiviral Activity. J Interferon Cytokine Res 2019; 39:283-292. [PMID: 30920934 DOI: 10.1089/jir.2018.0135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Type I interferons (IFNs) signal by forming a high affinity IFN-IFNAR2 dimer, which subsequently recruits IFNAR1 to form a ternary complex that initiates JAK/STAT signaling. Among the 12 IFNα subtypes, IFNα1 has a uniquely low affinity for IFNAR2 (<100 × of the other IFNα subtypes) and commensurately weak antiviral activity, suggesting an undefined function distinct from suppression of viral infections. Also unique in IFNα1 is substitution of a serine for phenylalanine at position 27, a contact point that stabilizes the IFNα:IFNAR2 hydrophobic interface. To determine whether IFNα1-S27 contributes to the low affinity for IFNAR2, we created an IFNα1 mutein, IFNα1-S27F, and compared it to wild-type IFNα1 and IFNα2. Substitution of phenylalanine for serine increased affinity for IFNAR2 ∼4-fold and commensurately enhanced activation of STAT1, STAT3, and STAT5, transcription of a subset of interferon stimulated genes, and restriction of vesicular stomatitis virus infection in vitro. Structural modeling suggests that S27 of IFNα1 disrupts the IFNα:IFNAR2 hydrophobic interface that is otherwise stabilized by F27 and that replacing S27 with phenylalanine partially restores the hydrophobic surface. Disruption of the hydrophobic IFNα:IFNAR2 interface by the unique S27 of IFN α1 contributes to its low affinity and weak antiviral activity.
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Affiliation(s)
- Nikunj Sharma
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Anya J O'Neal
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Christian Gonzalez
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Megen Wittling
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Erisa Gjinaj
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Lisa M Parsons
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Debasis Panda
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Alexey Khalenkov
- 2 Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Dorothy Scott
- 2 Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Saurav Misra
- 3 Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Ronald L Rabin
- 1 Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland
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Ammous-Boukhris N, Mosbah A, Ayadi W, Sahli E, Chevance S, Bondon A, Gargouri A, Baudy-Floc'h M, Mokdad-Gargouri R. B1.12: a novel peptide interacting with the extracellular loop of the EBV oncoprotein LMP1. Sci Rep 2019; 9:4389. [PMID: 30867462 PMCID: PMC6416395 DOI: 10.1038/s41598-019-39732-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
Latent membrane protein 1 (LMP1) encoded by the Epstein-Barr virus (EBV) plays an important role in EBV-induced cell transformation. Down-regulation of the LMP1 expression had shown promising results on cancer cell therapy. In this study, we identified by Phage display a novel peptide called B1.12 (ACPLDLRSPCG) which selectively binds to the extracellular loop (B1) of the LMP1 oncoprotein as demonstrated by molecular docking, NMR and ITC. Using an LMP1 expressing cell line, we showed that B1.12 decreased cell viability, and induced G0/G1 cell cycle arrest. In addition, the expression of A20, pAkt, and pNFkb (pRelA536) in C666-1 cells treated with B1.12 decreased compared to the untreated cells. In conclusion, we selected a novel peptide able to bind specifically to the extracellular loop of LMP1 and thus modulate its oncogenic properties.
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Affiliation(s)
- Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, Laboratory: Molecular Biotechnology of Eukaryotes, University of Sfax, Sfax, Tunisia
| | - Amor Mosbah
- BVBGR-LR 11ES31, ISBST, University of Manouba, Biotechnopole Sidi Thabet, 2020, Ariana, Tunisia
| | - Wajdi Ayadi
- Center of Biotechnology of Sfax, Laboratory: Molecular Biotechnology of Eukaryotes, University of Sfax, Sfax, Tunisia
| | - Emna Sahli
- Center of Biotechnology of Sfax, Plate-forme of Analysis, University of Sfax, Sfax, Tunisia
| | - Soizic Chevance
- COrInt, ISCR UMR CNRS 6226, Université de Rennes 1, Rennes, France
| | - Arnaud Bondon
- COrInt, ISCR UMR CNRS 6226, Université de Rennes 1, Rennes, France.,Plate-forme PRISM, Biosit, SFR UMS CNRS 3480 - INSERM 018, Université de Rennes 1, Rennes, France
| | - Ali Gargouri
- Center of Biotechnology of Sfax, Laboratory: Molecular Biotechnology of Eukaryotes, University of Sfax, Sfax, Tunisia
| | | | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, Laboratory: Molecular Biotechnology of Eukaryotes, University of Sfax, Sfax, Tunisia.
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118
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Sonntag Y, Gena P, Maggio A, Singh T, Artner I, Oklinski MK, Johanson U, Kjellbom P, Nieland JD, Nielsen S, Calamita G, Rützler M. Identification and characterization of potent and selective aquaporin-3 and aquaporin-7 inhibitors. J Biol Chem 2019; 294:7377-7387. [PMID: 30862673 DOI: 10.1074/jbc.ra118.006083] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
The aquaglyceroporins are a subfamily of aquaporins that conduct both water and glycerol. Aquaporin-3 (AQP3) has an important physiological function in renal water reabsorption, and AQP3-mediated hydrogen peroxide (H2O2) permeability can enhance cytokine signaling in several cell types. The related aquaglyceroporin AQP7 is required for dendritic cell chemokine responses and antigen uptake. Selective small-molecule inhibitors are desirable tools for investigating the biological and pathological roles of these and other AQP isoforms. Here, using a calcein fluorescence quenching assay, we screened a library of 7360 drug-like small molecules for inhibition of mouse AQP3 water permeability. Hit confirmation and expansion with commercially available substances identified the ortho-chloride-containing compound DFP00173, which inhibited mouse and human AQP3 with an IC50 of ∼0.1-0.4 μm but had low efficacy toward mouse AQP7 and AQP9. Surprisingly, inhibitor specificity testing revealed that the methylurea-linked compound Z433927330, a partial AQP3 inhibitor (IC50, ∼0.7-0.9 μm), is a potent and efficacious inhibitor of mouse AQP7 water permeability (IC50, ∼0.2 μm). Stopped-flow light scattering measurements confirmed that DFP00173 and Z433927330 inhibit AQP3 glycerol permeability in human erythrocytes. Moreover, DFP00173, Z433927330, and the previously identified AQP9 inhibitor RF03176 blocked aquaglyceroporin H2O2 permeability. Molecular docking to AQP3, AQP7, and AQP9 homology models suggested interactions between these inhibitors and aquaglyceroporins at similar binding sites. DFP00173 and Z433927330 constitute selective and potent AQP3 and AQP7 inhibitors, respectively, and contribute to a set of isoform-specific aquaglyceroporin inhibitors that will facilitate the evaluation of these AQP isoforms as drug targets.
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Affiliation(s)
- Yonathan Sonntag
- From the Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Patrizia Gena
- the Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari "Aldo Moro," 70125 Bari, Italy
| | - Anna Maggio
- the Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari "Aldo Moro," 70125 Bari, Italy
| | - Tania Singh
- the Stem Cell Center, Lund University, 22184 Lund, Sweden, and
| | - Isabella Artner
- the Stem Cell Center, Lund University, 22184 Lund, Sweden, and
| | - Michal K Oklinski
- the Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Urban Johanson
- From the Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Per Kjellbom
- From the Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - John Dirk Nieland
- the Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Søren Nielsen
- the Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Giuseppe Calamita
- the Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari "Aldo Moro," 70125 Bari, Italy
| | - Michael Rützler
- the Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
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119
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Banerjee A, Ray S. Molecular interactions and mutational impact upon rhodopsin (G90→D90) for hindering dark adaptation of eye: A comparative structural level outlook for signaling mechanism in night blindness. Mutat Res 2019; 814:7-14. [PMID: 30659944 DOI: 10.1016/j.mrfmmm.2019.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/17/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
For night blindness, a detailed structural exploration of the interactions among G-protein receptor rhodopsin, transducin and arrestin was performed. Rhodopsin is responsible for dim light vision while a point mutation (G90→D90) results in an adverse change in its photo-transduction. The validated 3D models of the three proteins were utilized, and upon mutation and interactions, rhodopsin attained higher stability (evaluated through thermodynamic energy calculations, electrostatic surface potential and solvent accessible area), thereby participating strongly with transducin. Conformational switches in mutated rhodopsin also depicted a firm conformation with few 310 helices accompanied by increased percentage of pure α-helices and sheets. All evaluations were corroborated through paired T-tests. Glu33 (glycosylated unit in the N-terminal zone) of rhodopsin plays a chief role in the overall interaction pattern. Arg69 and Glu33 from wild-type rhodopsin participated in ionic interactions, while the latter set of ionic interaction remained preserved even after mutation. Cys323 (C-terminal residue) and Arg69 formed H-bonds from the wild-type rhodopsin. Cys323 exceptionally supports cellular signaling pattern in the non-mutated situation and for the non-sufferers of night-blindness. Ser297 and Tyr43 from mutated rhodopsin reside in helices and interact with Thr32 of transducin, preserving the steady conformation in activated interacted state, even in the dark. Ser297 lies adjoined to Lys296 (retinal attachment site), which resides in NPXXY motif (an "activation switch" for signal transduction). Thus, the molecular facet for involvement of photo-transduction, which holds a paramount zone in ophthalmology, was dealt with. This might instigate the future prospect for drug discovery to prevent such mutations.
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Affiliation(s)
- Arundhati Banerjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India.
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
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120
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Hasan M, Ghosh PP, Azim KF, Mukta S, Abir RA, Nahar J, Hasan Khan MM. Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus. Microb Pathog 2019; 130:19-37. [PMID: 30822457 DOI: 10.1016/j.micpath.2019.02.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
Abstract
H7N9, a novel strain of avian origin influenza was the first recorded incidence where a human was transited by a N9 type influenza virus. Effective vaccination against influenza A (H7N9) is a major concern, since it has emerged as a life threatening viral pathogen. Here, an in silico reverse vaccinology strategy was adopted to design a unique chimeric subunit vaccine against avian influenza A (H7N9). Induction of humoral and cell-mediated immunity is the prime concerned characteristics for a peptide vaccine candidate, hence both T cell and B cell immunity of viral proteins were screened. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most antigenic epitopes of avian influenza A (H7N9) proteome. Further, a novel subunit vaccine was designed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, h ydrophilicity, theoretical PI and structural behavior. Homology modeling, refinement and validation of the designed vaccine allowed to construct a three dimensional structure of the predicted vaccine, further employed to molecular docking analysis with different MHC molecules and human immune TLR8 receptor present on lymphocyte cells. Moreover, disulfide engineering was employed to lessen the high mobility region of the designed vaccine in order to extend its stability. Furthermore, we investigated the molecular dynamic simulation of the modeled subunit vaccine and TLR8 complexed molecule to strengthen our prediction. Finally, the suggested vaccine was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for checking translational potency and microbial expression.
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Affiliation(s)
- Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
| | - Progga Paromita Ghosh
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Shamsunnahar Mukta
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Plant and Environmental Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Ruhshan Ahmed Abir
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Jannatun Nahar
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Mohammad Mehedi Hasan Khan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
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121
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In silico prediction of prolactin molecules as a tool for equine genomics reproduction. Mol Divers 2019; 23:1019-1028. [PMID: 30740642 DOI: 10.1007/s11030-018-09914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/31/2018] [Indexed: 10/27/2022]
Abstract
The prolactin hormone is involved in several biological functions, although its main role resides on reproduction. As it interferes on fertility changes, studies focused on human health have established a linkage of this hormone to fertility losses. Regarding animal research, there is still a lack of information about the structure of prolactin. In case of horse breeding, prolactin has a particular influence; once there is an individualization of these animals and equines are known for presenting several reproductive disorders. As there is no molecular structure available for the prolactin hormone and receptor, we performed several bioinformatics analyses through prediction and refinement softwares, as well as manual modifications. Aiming to elucidate the first computational structure of both molecules and analyse structural and functional aspects related to these proteins, here we provide the first known equine model for prolactin and prolactin receptor, which obtained high global quality scores in diverse software's for quality assessment. QMEAN overall score obtained for ePrl was (- 4.09) and QMEANbrane for ePrlr was (- 8.45), which proves the structures' reliability. This study will implement another tool in equine genomics in order to give light to interactions of these molecules, structural and functional alterations and therefore help diagnosing fertility problems, contributing in the selection of a high genetic herd.
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122
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Carpenter SM, Williams GJ. Extender Unit Promiscuity and Orthogonal Protein Interactions of an Aminomalonyl-ACP Utilizing Trans-Acyltransferase from Zwittermicin Biosynthesis. ACS Chem Biol 2018; 13:3361-3373. [PMID: 30484625 DOI: 10.1021/acschembio.8b00867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trans-acting acyltransferases (trans-ATs) are standalone enzymes that select and deliver extender units to polyketide synthase assembly lines. Accordingly, there is interest in leveraging trans-ATs as tools to regioselectively diversify polyketide structures. Yet, little is known regarding the extender unit and acyl carrier protein (ACP) specificity of trans-ATs, particularly those that utilize unusual ACP-linked extender units. For example, the biosynthesis of the antibiotic zwittermicin involves the trans-AT ZmaF, which is responsible for installing a rare ACP-linked aminomalonyl extender unit. Here, we developed a method to access a panel of non-natural and non-native ACP-linked extender units and used it to probe the promiscuity of ZmaF, revealing one of the most promiscuous ATs characterized to date. Furthermore, we demonstrated that ZmaF is highly orthogonal with respect to its ACP specificity, and the ability of ZmaF to trans-complement noncognate PKS modules was also explored. Together, these results set the stage for further engineering ZmaF as a tool for polyketide diversification.
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Affiliation(s)
- Samantha M. Carpenter
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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123
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Experimental accuracy in protein structure refinement via molecular dynamics simulations. Proc Natl Acad Sci U S A 2018; 115:13276-13281. [PMID: 30530696 DOI: 10.1073/pnas.1811364115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Refinement is the last step in protein structure prediction pipelines to convert approximate homology models to experimental accuracy. Protocols based on molecular dynamics (MD) simulations have shown promise, but current methods are limited to moderate levels of consistent refinement. To explore the energy landscape between homology models and native structures and analyze the challenges of MD-based refinement, eight test cases were studied via extensive simulations followed by Markov state modeling. In all cases, native states were found very close to the experimental structures and at the lowest free energies, but refinement was hindered by a rough energy landscape. Transitions from the homology model to the native states require the crossing of significant kinetic barriers on at least microsecond time scales. A significant energetic driving force toward the native state was lacking until its immediate vicinity, and there was significant sampling of off-pathway states competing for productive refinement. The role of recent force field improvements is discussed and transition paths are analyzed in detail to inform which key transitions have to be overcome to achieve successful refinement.
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124
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Zhang C, Wei X, Omenn GS, Zhang Y. Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. J Proteome Res 2018; 17:4186-4196. [PMID: 30265558 PMCID: PMC6438760 DOI: 10.1021/acs.jproteome.8b00453] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Understanding the function of human proteins is essential to decipher the molecular mechanisms of human diseases and phenotypes. Of the 17 470 human protein coding genes in the neXtProt 2018-01-17 database with unequivocal protein existence evidence (PE1), 1260 proteins do not have characterized functions. To reveal the function of poorly annotated human proteins, we developed a hybrid pipeline that creates protein structure prediction using I-TASSER and infers functional insights for the target protein from the functional templates recognized by COFACTOR. As a case study, the pipeline was applied to all 66 PE1 proteins with unknown or insufficiently specific function (uPE1) on human chromosome 17 as of neXtProt 2017-07-01. Benchmark testing on a control set of 100 well-characterized proteins randomly selected from the same chromosome shows high Gene Ontology (GO) term prediction accuracies of 0.69, 0.57, and 0.67 for molecular function (MF), biological process (BP), and cellular component (CC), respectively. Three pipelines of function annotations (homology detection, protein-protein interaction network inference, and structure template identification) have been exploited by COFACTOR. Detailed analyses show that structure template detection based on low-resolution protein structure prediction made the major contribution to the enhancement of the sensitivity and precision of the annotation predictions, especially for cases that do not have sequence-level homologous templates. For the chromosome 17 uPE1 proteins, the I-TASSER/COFACTOR pipeline confidently assigned MF, BP, and CC for 13, 33, and 49 proteins, respectively, with predicted functions ranging from sphingosine N-acyltransferase activity and sugar transmembrane transporter to cytoskeleton constitution. We highlight the 13 proteins with confident MF predictions; 11 of these are among the 33 proteins with confident BP predictions and 12 are among the 49 proteins with confident CC. This study demonstrates a novel computational approach to systematically annotate protein function in the human proteome and provides useful insights to guide experimental design and follow-up validation studies of these uncharacterized proteins.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Xiaoqiong Wei
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People’s Republic of China
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
- Departments of Internal Medicine and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
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125
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Compound heterozygous mutations in IL10RA combined with a complement factor properdin mutation in infantile-onset inflammatory bowel disease. Eur J Gastroenterol Hepatol 2018; 30:1491-1496. [PMID: 30199474 DOI: 10.1097/meg.0000000000001247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Inflammatory bowel diseases (IBDs) are chronic and multifactorial diseases resulting from a complex interaction of host genetic factors and environmental stimuli. Although many genome-wide association studies have identified host genetic factors associated with IBD, rare Mendelian forms of IBD have been reported in patients with very early onset forms. Therefore, this study aimed to identify genetic variants associated with infantile-onset IBD. PARTICIPANTS AND METHODS We obtained genomic DNA from whole blood samples of a male patient with infantile-onset IBD and nonconsanguineous Korean parents. Whole-exome sequencing was performed using trio samples. Then, we analyzed the data using susceptibility genes for monogenic forms of IBD and various immunodeficiencies and protein structural analysis. RESULTS The patient who presented with oral aphthous ulcers at the age of 14 days suffered from severe colitis and was refractory to medical treatment. Compound heterozygous mutations in IL10RA (p.R101W; p.T179T) were found in the patient. In addition, a hemizygous mutation in complement factor properdin (CFP) (p.L456V) located on the X-chromosome was detected, inherited from the patient's mother. Protein structural modeling suggested impaired properdin subunit interactions by p.L456V that may hamper protein oligomerization required for complement activation. CONCLUSION This study identified compound heterozygous mutations in IL10RA combined with a hemizygous CFP mutation in infantile-onset IBD by using whole-exome sequencing. CFP p.L456V may exacerbate symptoms of infantile-onset IBD by disturbing oligomerization of properdin.
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Mathematical model for plant-insect interaction with dynamic response to PAD4-BIK1 interaction and effect of BIK1 inhibition. Biosystems 2018; 175:11-23. [PMID: 30481546 DOI: 10.1016/j.biosystems.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/13/2018] [Accepted: 11/20/2018] [Indexed: 11/23/2022]
Abstract
Plant-insect interaction system is a widely studied model of the ecosystem. Numerical understanding of this counter system has developed from initial analogy based approach with a predator-prey model to its recent mathematical interpretation including plant immunity concept. In current work, we propose an extension to this model, including molecular interactions behind the plant defense system and its effect on ecological behaviour. Inspired from biomolecular interaction given by Louis and Shah in 2014, we propose here a mathematical model to depict molecular dependence and control of plant insect interaction system. Insect infestation mediated Botrytis Induced Kinase-1 (BIK1) induction resulted in inhibition of Phyto Alexin Deficient-4 (PAD4) protein. Lowered PAD4 triggers the plant defense mechanism, leading to degraded plant immune potential and thereby reducing the plant quality. We mathematically adapt these interactions to show their influence on plant-insect interaction system and hypothesize the significance of BIK1 inhibition leading to the improved plant quality. We implemented the plethora of computational modeling and all atom MD simulations to explain the Plant-Insect-PAD4-BIK1 interaction network and identify potential molecular mechanisms of plant improvement by BIK1 inhibition.
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Esfandiari N, Sefidbakht Y. An isolate of Potato Virus X capsid protein from N. benthamiana: Insights from homology modeling and molecular dynamics simulation. Int J Biol Macromol 2018; 116:939-946. [PMID: 29777803 DOI: 10.1016/j.ijbiomac.2018.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/17/2018] [Accepted: 05/08/2018] [Indexed: 12/16/2022]
Abstract
Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate. The capsid protein (CP) structure were modeled based on homology and subjected to three independent 80 ns molecular dynamics minimization (GROMACS, OPLS force field) in the SPC water box. The RMSD, RMSF, SASA, and electrostatic properties were retrieved from the trajectories. Flexibility and hydrophilic nature of the N-terminal residues (1-34) of solvated CP could be observed in conformational changes upon minimization. The obtained structure was then docked with NbPCIP1 using ClusPro 2.0. The strong binding affinity of these two proteins (≈-16.0 Kcal mol-1) represents the formation of inclusion body and hence appearance of the symptoms.
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Affiliation(s)
- Neda Esfandiari
- Protein Research Center, Shahid Beheshti University, G.C, Tehran, Iran.
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, G.C, Tehran, Iran.
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128
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Khan S, Guo TW, Misra S. A coevolution-guided model for the rotor of the bacterial flagellar motor. Sci Rep 2018; 8:11754. [PMID: 30082903 PMCID: PMC6079021 DOI: 10.1038/s41598-018-30293-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 01/17/2023] Open
Abstract
The Salmonella typhimurium trans-membrane FliF MS ring templates assembly of the rotary bacterial flagellar motor, which also contains a cytoplasmic C-ring. A full-frame fusion of FliF with the rotor protein FliG assembles rings in non-motile expression hosts. 3D electron microscopy reconstructions of these FliFFliG rings show three high electron-density sub-volumes. 3D-classification revealed heterogeneity of the assigned cytoplasmic volume consistent with FliG lability. We used residue coevolution to construct homodimer building blocks for ring assembly, with X-ray crystal structures from other species and injectisome analogs. The coevolution signal validates folds and, importantly, indicates strong homodimer contacts for three ring building motifs (RBMs), initially identified in injectisome structures. It also indicates that the cofolded domains of the FliG N-terminal domain (FliG_N) with embedded α-helical FliF carboxy-terminal tail homo-oligomerize. The FliG middle and C-terminal domains (FliG_MC) have a weak signal for homo-dimerization but have coevolved to conserve their stacking contact. The homodimers and their ring models fit well into the 3D reconstruction. We hypothesize that a stable FliF periplasmic hub provides a platform for FliG ring self-assembly, but the FliG_MC ring has only limited stability without the C-ring. We also present a mechanical model for torque transmission in the FliFFliG ring.
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Affiliation(s)
- Shahid Khan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Tai Wei Guo
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Saurav Misra
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
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129
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Deng H, Jia Y, Zhang Y. Protein structure prediction. INTERNATIONAL JOURNAL OF MODERN PHYSICS. B 2018; 32:1840009. [PMID: 30853739 PMCID: PMC6407873 DOI: 10.1142/s021797921840009x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.
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Affiliation(s)
- Haiyou Deng
- College of Science, Huazhong Agricultural University, Wuhan 4R0070, P. R. China
| | - Ya Jia
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, P. R. China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 45108, USA
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130
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Dutagaci B, Heo L, Feig M. Structure refinement of membrane proteins via molecular dynamics simulations. Proteins 2018; 86:738-750. [PMID: 29675899 PMCID: PMC6013386 DOI: 10.1002/prot.25508] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 12/12/2022]
Abstract
A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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131
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Yang Y, Adi T, Effraim PR, Chen L, Dib‐Hajj SD, Waxman SG. Reverse pharmacogenomics: carbamazepine normalizes activation and attenuates thermal hyperexcitability of sensory neurons due to Na v 1.7 mutation I234T. Br J Pharmacol 2018; 175:2261-2271. [PMID: 28658526 PMCID: PMC5980548 DOI: 10.1111/bph.13935] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/17/2017] [Accepted: 06/05/2017] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND PURPOSE Pharmacotherapy for pain currently involves trial and error. A previous study on inherited erythromelalgia (a genetic model of neuropathic pain due to mutations in the sodium channel, Nav 1.7) used genomics, structural modelling and biophysical and pharmacological analyses to guide pharmacotherapy and showed that carbamazepine normalizes voltage dependence of activation of the Nav 1.7-S241T mutant channel, reducing pain in patients carrying this mutation. However, whether this approach is applicable to other Nav channel mutants is still unknown. EXPERIMENTAL APPROACH We used structural modelling, patch clamp and multi-electrode array (MEA) recording to assess the effects of carbamazepine on Nav 1.7-I234T mutant channels and on the firing of dorsal root ganglion (DRG) sensory neurons expressing these mutant channels. KEY RESULTS In a reverse engineering approach, structural modelling showed that the I234T mutation is located in atomic proximity to the carbamazepine-responsive S241T mutation and that activation of Nav 1.7-I234T mutant channels, from patients who are known to respond to carbamazepine, is partly normalized with a clinically relevant concentration (30 μM) of carbamazepine. There was significantly higher firing in intact sensory neurons expressing Nav 1.7-I234T channels, compared with neurons expressing the normal channels (Nav 1.7-WT). Pre-incubation with 30 μM carbamazepine also significantly reduced the firing of intact DRG sensory neurons expressing Nav 1.7-I234T channels. Although the expected use-dependent inhibition of Nav 1.7-WT channels by carbamazepine was confirmed, carbamazepine did not enhance use-dependent inhibition of Nav 1.7-I234T mutant channels. CONCLUSION AND IMPLICATIONS These results support the utility of a pharmacogenomic approach to treatment of pain in patients carrying sodium channel variants. LINKED ARTICLES This article is part of a themed section on Recent Advances in Targeting Ion Channels to Treat Chronic Pain. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.12/issuetoc.
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Affiliation(s)
- Yang Yang
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
| | - Talia Adi
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
| | - Philip R Effraim
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
- Department of AnesthesiologyYale University School of MedicineNew HavenCTUSA
| | - Lubin Chen
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
| | - Sulayman D Dib‐Hajj
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
| | - Stephen G Waxman
- Department of NeurologyYale University School of MedicineNew HavenCTUSA
- Center for Neuroscience and Regeneration ResearchYale University School of MedicineNew HavenCTUSA
- Rehabilitation Research CenterVA Connecticut Healthcare SystemWest HavenCTUSA
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132
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Human transbodies that interfere with the functions of Ebola virus VP35 protein in genome replication and transcription and innate immune antagonism. Emerg Microbes Infect 2018; 7:41. [PMID: 29568066 PMCID: PMC5864874 DOI: 10.1038/s41426-018-0031-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 01/10/2023]
Abstract
Small molecular inhibitors and passive immunization against Ebola virus disease (EVD) have been tested in animal models, including rodents and non-human primates, as well as in clinical trials. Nevertheless, there is currently no Food and Drug Administration (FDA)-approved therapy, and alternative strategies must be pursued. The aim of this study was to produce cell-penetrable human single-chain antibodies (transbodies) that are able to interfere with the activities of interferon inhibitory domain (IID) of the VP35 protein, a multifunctional virulence factor of Ebola virus (EBOV). We speculated that effective VP35-IID-specific transbodies could inspire further studies to identify an alternative to conventional antibody therapies. Phage display technology was used to generate Escherichia coli-derived human single-chain antibodies (HuscFvs) that bind to IID. HuscFvs were linked to nona-arginine (R9) to make them cell penetrable. Transbodies of transformed E. coli clones 13 and 3, which were predicted to interact with first basic patch residues (R9-HuscFv13), central basic patch, and end-cap residues (R9-HuscFv3), effectively inhibited EBOV minigenome activity. Transbodies of E. coli clones 3 and 8 antagonized VP35-mediated interferon suppression in VP35-transduced cells. We postulate that these transbodies formed an interface contact with the IID central basic patch, end-cap, and/or residues that are important for IID multimeric formation for dsRNA binding. These transbodies should be evaluated further in vitro using authentic EBOV and in vivo in animal models of EVD before their therapeutic/prophylactic effectiveness is clinically evaluated.
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133
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Heo L, Feig M. PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinformatics 2018; 34:1063-1065. [PMID: 29126101 PMCID: PMC5860225 DOI: 10.1093/bioinformatics/btx726] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/04/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Abstract
Summary Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. Availability and implementation PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. Contact feig@msu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lim Heo
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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134
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Mallika V, Sivakumar KC, Aiswarya G, Soniya EV. In silico approaches illustrate the evolutionary pattern and protein-small molecule interactions of quinolone synthase from Aegle marmelos Correa. J Biomol Struct Dyn 2018; 37:195-209. [PMID: 29308712 DOI: 10.1080/07391102.2017.1422991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a Rutacean-specific plant type III polyketide synthase that synthesizes quinolone, acridone, and benzalacetone with therapeutic potential. Simple architecture and broad substrate affinity of AmQNS make it as one of the target enzymes to produce novel structural scaffolds. Another unique feature of AmQNS despite its high similarity to acridone forming type III polyketide synthase from Citrus microcarpa is the variation in the product formation. Hence, to explore the characteristic features of AmQNS, an in-depth sequence and structure-based bioinformatics analyses were performed. Our studies indicated that AmQNS and its nearest homologs have evolved by a series of gene duplication events and strong purifying selection pressure constrains them in the evolutionary process. Additionally, some amino acid alterations were identified in the functionally important region(s), which can contribute to the functional divergence of the enzyme. Prediction of favorable amino acid substitutions will be advantageous in the metabolic engineering of AmQNS for the production of novel compounds. Furthermore, comparative modeling and docking studies were utilized to investigate the structural behavior and small molecule interaction pattern of AmQNS. The observations and results reported here are crucial for advancing our understanding of AmQNS's phylogenetic position, selection pressure, evolvability, interaction pattern and thus providing the foundation for further studies on the structural and reaction mechanism.
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Affiliation(s)
- V Mallika
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - K C Sivakumar
- b Bioinformatics Facility , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - G Aiswarya
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - E V Soniya
- a Plant Disease Biology & Biotechnology Division , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
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135
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Gómez-Escudero J, Moreno V, Martín-Alonso M, Hernández-Riquer MV, Feinberg T, Colmenar Á, Calvo E, Camafeita E, Martínez F, Oudhoff MJ, Weiss SJ, Arroyo AG. E-cadherin cleavage by MT2-MMP regulates apical junctional signaling and epithelial homeostasis in the intestine. J Cell Sci 2017; 130:4013-4027. [PMID: 29061881 PMCID: PMC5769589 DOI: 10.1242/jcs.203687] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022] Open
Abstract
Cadherin-based intercellular adhesions are essential players in epithelial homeostasis, but their dynamic regulation during tissue morphogenesis and remodeling remain largely undefined. Here, we characterize an unexpected role for the membrane-anchored metalloproteinase MT2-MMP in regulating epithelial cell quiescence. Following co-immunoprecipitation and mass spectrometry, the MT2-MMP cytosolic tail was found to interact with the zonula occludens protein-1 (ZO-1) at the apical junctions of polarized epithelial cells. Functionally, MT2-MMP localizes in the apical domain of epithelial cells where it cleaves E-cadherin and promotes epithelial cell accumulation, a phenotype observed in 2D polarized cells as well as 3D cysts. MT2-MMP-mediated cleavage subsequently disrupts apical E-cadherin-mediated cell quiescence resulting in relaxed apical cortical tension favoring cell extrusion and re-sorting of Src kinase activity to junctional complexes, thereby promoting proliferation. Physiologically, MT2-MMP loss of function alters E-cadherin distribution, leading to impaired 3D organoid formation by mouse colonic epithelial cells ex vivo and reduction of cell proliferation within intestinal crypts in vivo Taken together, these studies identify an MT2-MMP-E-cadherin axis that functions as a novel regulator of epithelial cell homeostasis in vivo.
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Affiliation(s)
- Jesús Gómez-Escudero
- Matrix Metalloproteinases in Angiogenesis and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Vanessa Moreno
- Matrix Metalloproteinases in Angiogenesis and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Mara Martín-Alonso
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - M Victoria Hernández-Riquer
- Matrix Metalloproteinases in Angiogenesis and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Tamar Feinberg
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ángel Colmenar
- Matrix Metalloproteinases in Angiogenesis and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Enrique Calvo
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Emilio Camafeita
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Fernando Martínez
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Menno J Oudhoff
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Stephen J Weiss
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alicia G Arroyo
- Matrix Metalloproteinases in Angiogenesis and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
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136
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Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter. Sci Rep 2017; 7:15743. [PMID: 29147015 PMCID: PMC5691160 DOI: 10.1038/s41598-017-15837-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 11/23/2022] Open
Abstract
Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint. Two proteins, FlgK and FlgL, assure a smooth connectivity between the hook and the filament. Here we show that, in Campylobacter, the 3D structure of FlgK differs from that of its orthologs in Salmonella and Burkholderia, whose structures have previously been solved. Docking the model of the FlgK junction onto the structure of the Campylobacter hook provides some clues about its divergence. These data suggest how evolutionary pressure to adapt to structural constraints, due to the structure of Campylobacter hook, causes divergence of one element of a supra-molecular complex in order to maintain the function of the entire flagellar assembly.
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137
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Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins 2017; 86 Suppl 1:136-151. [PMID: 29082551 DOI: 10.1002/prot.25414] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/09/2017] [Accepted: 10/27/2017] [Indexed: 12/26/2022]
Abstract
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM-score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non-foldable to foldable (TM-score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue-level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi-domain proteins and folding of β-proteins with complicated topologies bound by long-range strand-strand interactions. Improvements on domain boundary and long-range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - S M Mortuza
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Baoji He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Yanting Wang
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
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138
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Dapkūnas J, Olechnovič K, Venclovas Č. Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection. Proteins 2017; 86 Suppl 1:292-301. [DOI: 10.1002/prot.25378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/25/2017] [Accepted: 09/10/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Justas Dapkūnas
- Institute of Biotechnology, Vilnius University, Saulėtekio 7; Vilnius LT-10257 Lithuania
| | - Kliment Olechnovič
- Institute of Biotechnology, Vilnius University, Saulėtekio 7; Vilnius LT-10257 Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Saulėtekio 7; Vilnius LT-10257 Lithuania
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139
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Berenger F, Simoncini D, Voet A, Shrestha R, Zhang KYJ. Fragger: a protein fragment picker for structural queries. F1000Res 2017; 6:1722. [PMID: 29399321 PMCID: PMC5773926 DOI: 10.12688/f1000research.12486.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2018] [Indexed: 12/02/2022] Open
Abstract
Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.
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Affiliation(s)
- Francois Berenger
- System Cohort Division, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, KU Leuven, Heverlee, Belgium
| | - Rojan Shrestha
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, Yokohama, Kanagawa, Japan
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140
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Bulldan A, Malviya VN, Upmanyu N, Konrad L, Scheiner-Bobis G. Testosterone/bicalutamide antagonism at the predicted extracellular androgen binding site of ZIP9. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2402-2414. [PMID: 28943399 DOI: 10.1016/j.bbamcr.2017.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
Abstract
ZIP9 is a Zn2+ transporter, testosterone receptor, and mediator of signaling events through G-proteins. Despite these pivotal properties, however, its physiological and pathophysiological significance has not yet been comprehensively addressed. Using a cell line that lacks the classical androgen receptor we show that ZIP9-mediated phosphorylation of Erk1/2, CREB, or ATF-1 and expression of claudin-5 and zonula occludens-1 by testosterone can be completely antagonized by bicalutamide (Casodex), an anti-androgen of significant clinical impact. Computational modeling and docking experiments with ZIP9 reveal typical characteristics of ZIP transporters and an extracellular binding site for testosterone capable of accommodating bicalutamide. The presence of this site is verified by our demonstration that the membrane-impermeable testosterone analogue T-BSA-FITC labels the membrane only when ZIP9 is expressed and that this labeling is completely prevented by bicalutamide. The study connects structural features of ZIP9 to its functions and indicates a possible relevance of ZIP9 as a pharmacological target.
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Affiliation(s)
- Ahmed Bulldan
- Institute for Veterinary-Physiology and -Biochemistry, School of Veterinary Medicine, Justus-Liebig-University, Giessen, Germany
| | | | - Neha Upmanyu
- Institute for Veterinary-Physiology and -Biochemistry, School of Veterinary Medicine, Justus-Liebig-University, Giessen, Germany
| | - Lutz Konrad
- Department of Obstetrics and Gynecology, Faculty of Medicine, Justus-Liebig-University, Giessen, Germany
| | - Georgios Scheiner-Bobis
- Institute for Veterinary-Physiology and -Biochemistry, School of Veterinary Medicine, Justus-Liebig-University, Giessen, Germany.
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141
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Cheng Q, Joung I, Lee J. A Simple and Efficient Protein Structure Refinement Method. J Chem Theory Comput 2017; 13:5146-5162. [PMID: 28800396 DOI: 10.1021/acs.jctc.7b00470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Improving the quality of a given protein structure can serve as the ultimate solution for accurate protein structure prediction, and seeking such a method is currently a challenge in computational structural biology. In order to promote and encourage much needed such efforts, CASP (Critical Assessment of Structure Prediction) has been providing an ideal computational experimental platform, where it was reported only recently (since CASP10) that systematic protein structure refinement is possible by carrying out extensive (approximately millisecond) MD simulations with proper restraints generated from the given structure. Using an explicit solvent model and much reduced positional and distance restraints than previously exercised, we propose a refinement protocol that combines a series of short (5 ns) MD simulations with energy minimization procedures. Testing and benchmarking on 54 CASP8-10 refinement targets and 34 CASP11 refinement targets shows quite promising results. Using only a small fraction of MD simulation steps (nanosecond versus millisecond), systematic protein structure refinement was demonstrated in this work, indicating that refinement of a given model can be achieved using a few hours of desktop computing.
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Affiliation(s)
- Qianyi Cheng
- Center for In Silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Korea
| | - InSuk Joung
- Center for In Silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Korea
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142
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Liu L, Zhang Z, Shao CL, Wang CY. Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases. Front Microbiol 2017; 8:1685. [PMID: 28928723 PMCID: PMC5591372 DOI: 10.3389/fmicb.2017.01685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/21/2017] [Indexed: 11/14/2022] Open
Abstract
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE). The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong UniversityJinan, China
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of ChinaQingdao, China
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143
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Ciemny MP, Kurcinski M, Blaszczyk M, Kolinski A, Kmiecik S. Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif. Biomed Eng Online 2017; 16:71. [PMID: 28830442 PMCID: PMC5568603 DOI: 10.1186/s12938-017-0362-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Many protein–protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In this work, we test a possibility of using flexible docking of a short linear motif to predict the interaction interface of the EphB4-EphrinB2 complex (a system extensively studied for its significance in tumor progression). Methods In the modeling, we only use knowledge about the motif sequence and experimental structures of EphB4-EphrinB2 complex partners. The proposed protocol enables efficient modeling of significant conformational changes in the short linear motif fragment during molecular docking simulation. For the docking simulations, we use the CABS-dock method for docking fully flexible peptides to flexible protein receptors (available as a server at http://biocomp.chem.uw.edu.pl/CABSdock/). Based on the docking result, the protein–protein complex is reconstructed and refined. Results Using this novel protocol, we obtained an accurate EphB4-EphrinB2 interaction model. Conclusions The results show that the CABS-dock method may be useful as the primary docking tool in specific protein–protein docking cases similar to EphB4-EphrinB2 complex—that is, where a short linear motif fragment can be identified.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
| | - Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Maciej Blaszczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
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144
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DiGiacomo V, de Opakua AI, Papakonstantinou MP, Nguyen LT, Merino N, Blanco-Canosa JB, Blanco FJ, Garcia-Marcos M. The Gαi-GIV binding interface is a druggable protein-protein interaction. Sci Rep 2017; 7:8575. [PMID: 28819150 PMCID: PMC5561080 DOI: 10.1038/s41598-017-08829-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 01/26/2023] Open
Abstract
Heterotrimeric G proteins are usually activated by the guanine-nucleotide exchange factor (GEF) activity of GPCRs. However, some non-receptor proteins are also GEFs. GIV (a.k.a Girdin) was the first non-receptor protein for which the GEF activity was ascribed to a well-defined protein sequence that directly binds Gαi. GIV expression promotes metastasis and disruption of its binding to Gαi blunts the pro-metastatic behavior of cancer cells. Although this suggests that inhibition of the Gαi-GIV interaction is a promising therapeutic strategy, protein-protein interactions (PPIs) are considered poorly "druggable" targets requiring case-by-case validation. Here, we set out to investigate whether Gαi-GIV is a druggable PPI. We tested a collection of >1,000 compounds on the Gαi-GIV PPI by in silico ligand screening and separately by a chemical high-throughput screening (HTS) assay. Two hits, ATA and NF023, obtained in both screens were confirmed in secondary HTS and low-throughput assays. The binding site of NF023, identified by NMR spectroscopy and biochemical assays, overlaps with the Gαi-GIV interface. Importantly, NF023 did not disrupt Gαi-Gβγ binding, indicating its specificity toward Gαi-GIV. This work establishes the Gαi-GIV PPI as a druggable target and sets the conceptual and technical framework for the discovery of novel inhibitors of this PPI.
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Affiliation(s)
- Vincent DiGiacomo
- Department of Biochemistry, Boston University School of Medicine, Boston, USA
| | | | | | - Lien T Nguyen
- Department of Biochemistry, Boston University School of Medicine, Boston, USA
| | | | - Juan B Blanco-Canosa
- Department of Chemistry and Molecular Pharmacology, IRB Barcelona, Barcelona, Spain
| | - Francisco J Blanco
- CIC-BioGune, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Mikel Garcia-Marcos
- Department of Biochemistry, Boston University School of Medicine, Boston, USA.
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145
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Lam SD, Das S, Sillitoe I, Orengo C. An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol 2017; 73:628-640. [PMID: 28777078 PMCID: PMC5571743 DOI: 10.1107/s2059798317008920] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/14/2017] [Indexed: 12/02/2022] Open
Abstract
Computational modelling of proteins has been a major catalyst in structural biology. Bioinformatics groups have exploited the repositories of known structures to predict high-quality structural models with high efficiency at low cost. This article provides an overview of comparative modelling, reviews recent developments and describes resources dedicated to large-scale comparative modelling of genome sequences. The value of subclustering protein domain superfamilies to guide the template-selection process is investigated. Some recent cases in which structural modelling has aided experimental work to determine very large macromolecular complexes are also cited.
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Affiliation(s)
- Su Datt Lam
- Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, London WC1E 6BT, England
- School of Biosciences and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Sayoni Das
- Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, London WC1E 6BT, England
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, London WC1E 6BT, England
| | - Christine Orengo
- Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, London WC1E 6BT, England
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146
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Dakal TC, Kala D, Dhiman G, Yadav V, Krokhotin A, Dokholyan NV. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. Sci Rep 2017; 7:6525. [PMID: 28747718 PMCID: PMC5529537 DOI: 10.1038/s41598-017-06575-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 06/14/2017] [Indexed: 01/19/2023] Open
Abstract
Here we report an in-silico approach for identification, characterization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using three steps. In first step, sequence homology-based genetic analysis of a set of 50 coding SNPs associated with 41 rsIDs using SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer) identified 23 nsSNPs to be putatively damaging/deleterious in at least one of the two tools used. Subsequently, structure-homology based PolyPhen-2 (Polymorphism Phenotyping) analysis predicted 9 of 23 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P and V88D) to be damaging. According to the conditional hypothesis for the study, only nsSNPs that score damaging/deleterious prediction in both sequence and structural homology-based approach will be considered as 'high-confidence' nsSNPs. In step 2, based on conservation of amino acid residues, stability analysis, structural superimposition, RSMD and docking analysis, the possible structural-functional relationship was ascertained for high-confidence nsSNPs. Finally, in a separate analysis (step 3), the IL-8 deregulation has also appeared to be an important prognostic marker for detection of patients with gastric and lung cancer. This study, for the first time, provided in-depth insights on the effects of amino acid substitutions on IL-8 protein structure, function and disease association.
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Affiliation(s)
- Tikam Chand Dakal
- Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, 303007, Rajasthan, India.
| | - Deepak Kala
- University Institute of Biopharma Sciences, Chandigarh University, Mohali, 140413, Punjab, India
| | - Gourav Dhiman
- University Institute of Biopharma Sciences, Chandigarh University, Mohali, 140413, Punjab, India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, 123029, Haryana, India
| | - Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
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147
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Ding Y, Zhao W, Zhang T, Qiang H, Lu J, Su X, Wen S, Xu F, Zhang M, Zhang H, Zeng C, Liu Z, Chen H. A haplotype in CFH family genes confers high risk of rare glomerular nephropathies. Sci Rep 2017; 7:6004. [PMID: 28729648 PMCID: PMC5519609 DOI: 10.1038/s41598-017-05173-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/24/2017] [Indexed: 12/15/2022] Open
Abstract
Despite distinct renal lesions, a series of rare glomerular nephropathies are reportedly mediated by complement overactivation. Genetic variations in complement genes contribute to disease risk, but the relationship of genotype to phenotype has not been straightforward. Here, we screened 11 complement genes from 91 patients with atypical hemolytic uremic syndrome (aHUS), C3 glomerulopathy (C3G) and membranoproliferative glomerulonephritis type I (MPGN I), and identified the concomitant presence of three missense variations located within the human complement Factor H (CFH) gene cluster. The three variations, rs55807605, rs61737525 and rs57960694, have strong linkage disequilibrium; subsequent haplotype analysis indicated that ATA increased the susceptibility of these renal diseases. In silico analysis, the CFHR3 rs61737525-T risk allele altered the physical and structural properties and generated a reduction in binding affinity of the CFHR3/C3b complex. Surface plasmon resonance (SPR) binding analysis further demonstrated the substitution induced a decrease of two orders of magnitude in C3b-binding properties, with a declined cofactor activity in fluid phase. These data suggest that the haplotype carrying the causative allele behaves as a partial C3 convertase deficiency, predisposing individuals to diverse pathologic lesions underlying complement overactivation. Such genotype-phenotype discrepancies allow better understanding about these nephropathies mediated by genetic complement disorders.
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Affiliation(s)
- Yin Ding
- Devision of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Weiwei Zhao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Tao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Hao Qiang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Jianping Lu
- Devision of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Xin Su
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Shuzhen Wen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Feng Xu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Haitao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Zhihong Liu
- Devision of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China. .,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.
| | - Huimei Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.
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148
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Nav1.7-A1632G Mutation from a Family with Inherited Erythromelalgia: Enhanced Firing of Dorsal Root Ganglia Neurons Evoked by Thermal Stimuli. J Neurosci 2017; 36:7511-22. [PMID: 27413160 DOI: 10.1523/jneurosci.0462-16.2016] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/06/2016] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Voltage-gated sodium channel Nav1.7 is a central player in human pain. Mutations in Nav1.7 produce several pain syndromes, including inherited erythromelalgia (IEM), a disorder in which gain-of-function mutations render dorsal root ganglia (DRG) neurons hyperexcitable. Although patients with IEM suffer from episodes of intense burning pain triggered by warmth, the effects of increased temperature on DRG neurons expressing mutant Nav1.7 channels have not been well documented. Here, using structural modeling, voltage-clamp, current-clamp, and multielectrode array recordings, we have studied a newly identified Nav1.7 mutation, Ala1632Gly, from a multigeneration family with IEM. Structural modeling suggests that Ala1632 is a molecular hinge and that the Ala1632Gly mutation may affect channel gating. Voltage-clamp recordings revealed that the Nav1.7-A1632G mutation hyperpolarizes activation and depolarizes fast-inactivation, both gain-of-function attributes at the channel level. Whole-cell current-clamp recordings demonstrated increased spontaneous firing, lower current threshold, and enhanced evoked firing in rat DRG neurons expressing Nav1.7-A1632G mutant channels. Multielectrode array recordings further revealed that intact rat DRG neurons expressing Nav1.7-A1632G mutant channels are more active than those expressing Nav1.7 WT channels. We also showed that physiologically relevant thermal stimuli markedly increase the mean firing frequencies and the number of active rat DRG neurons expressing Nav1.7-A1632G mutant channels, whereas the same thermal stimuli only increase these parameters slightly in rat DRG neurons expressing Nav1.7 WT channels. The response of DRG neurons expressing Nav1.7-A1632G mutant channels upon increase in temperature suggests a cellular basis for warmth-triggered pain in IEM. SIGNIFICANCE STATEMENT Inherited erythromelalgia (IEM), a severe pain syndrome characterized by episodes of intense burning pain triggered by warmth, is caused by mutations in sodium channel Nav1.7, which are preferentially expressed in sensory and sympathetic neurons. More than 20 gain-of-function Nav1.7 mutations have been identified from IEM patients, but the question of how warmth triggers episodes of pain in IEM has not been well addressed. Combining multielectrode array, voltage-clamp, and current-clamp recordings, we assessed a newly identified IEM mutation (Nav1.7-A1632G) from a multigeneration family. Our data demonstrate gain-of-function attributes at the channel level and differential effects of physiologically relevant thermal stimuli on the excitability of DRG neurons expressing mutant and WT Nav1.7 channels, suggesting a cellular mechanism for warmth-triggered pain episodes in IEM patients.
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149
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Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V. A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science 2017; 357:605-609. [PMID: 28663439 DOI: 10.1126/science.aao0100] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 12/26/2022]
Abstract
Type III CRISPR-Cas systems in prokaryotes provide immunity against invading nucleic acids through the coordinated degradation of transcriptionally active DNA and its transcripts by the Csm effector complex. The Cas10 subunit of the complex contains an HD nuclease domain that is responsible for DNA degradation and two Palm domains with elusive functions. In addition, Csm6, a ribonuclease that is not part of the complex, is also required to provide full immunity. We show here that target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates (cA n ; n = 2 to 6) by means of the Palm domains. Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation.
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Affiliation(s)
- Migle Kazlauskiene
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania.
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150
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Hou QL, Luo JX, Zhang BC, Jiang GF, Ding W, Zhang YQ. 3D-QSAR and Molecular Docking Studies on the TcPMCA1-Mediated Detoxification of Scopoletin and Coumarin Derivatives. Int J Mol Sci 2017; 18:E1380. [PMID: 28653986 PMCID: PMC5535873 DOI: 10.3390/ijms18071380] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 12/14/2022] Open
Abstract
The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is an economically important agricultural pest that is difficult to prevent and control. Scopoletin is a botanical coumarin derivative that targets Ca2+-ATPase to exert a strong acaricidal effect on carmine spider mites. In this study, the full-length cDNA sequence of a plasma membrane Ca2+-ATPase 1 gene (TcPMCA1) was cloned. The sequence contains an open reading frame of 3750 bp and encodes a putative protein of 1249 amino acids. The effects of scopoletin on TcPMCA1 expression were investigated. TcPMCA1 was significantly upregulated after it was exposed to 10%, 30%, and 50% of the lethal concentration of scopoletin. Homology modeling, molecular docking, and three-dimensional quantitative structure-activity relationships were then studied to explore the relationship between scopoletin structure and TcPMCA1-inhibiting activity of scopoletin and other 30 coumarin derivatives. Results showed that scopoletin inserts into the binding cavity and interacts with amino acid residues at the binding site of the TcPMCA1 protein through the driving forces of hydrogen bonds. Furthermore, CoMFA (comparative molecular field analysis)- and CoMSIA (comparative molecular similarity index analysis)-derived models showed that the steric and H-bond fields of these compounds exert important influences on the activities of the coumarin compounds.Notably, the C3, C6, and C7 positions in the skeletal structure of the coumarins are the most suitable active sites. This work provides insights into the mechanism underlying the interaction of scopoletin with TcPMCA1. The present results can improve the understanding on plasma membrane Ca2+-ATPase-mediated (PMCA-mediated) detoxification of scopoletin and coumarin derivatives in T. cinnabarinus, as well as provide valuable information for the design of novel PMCA-inhibiting acaricides.
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Affiliation(s)
- Qiu-Li Hou
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
| | - Jin-Xiang Luo
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
| | - Bing-Chuan Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
| | - Gao-Fei Jiang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
| | - Yong-Qiang Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
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