151
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Motlova L, Klimova N, Fiser R, Sebo P, Bumba L. Continuous Assembly of β-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (RTX) Proteins. J Mol Biol 2020; 432:5696-5710. [PMID: 32860773 DOI: 10.1016/j.jmb.2020.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 01/10/2023]
Abstract
Repeats-in-Toxin (RTX) proteins of Gram-negative bacteria are excreted through the type I secretion system (T1SS) that recognizes non-cleavable C-terminal secretion signals. These are preceded by arrays of glycine and aspartate-rich nonapeptide repeats grouped by four to eight β strands into blocks that fold into calcium-binding parallel β-roll structures. The β-rolls are interspersed by linkers of variable length and sequence and the organization of multiple RTX repeat blocks within large RTX domains remains unknown. Here we examined the structure and function of the RTX domain of Bordetella pertussis adenylate cyclase toxin (CyaA) that is composed of five β-roll RTX blocks. We show that the non-folded RTX repeats maintain the stability of the CyaA polypeptide in the Ca2+-depleted bacterial cytosol and thereby enable its efficient translocation through the T1SS apparatus. The efficacy of secretion of truncated CyaA constructs was dictated by the number of retained RTX repeat blocks and depended on the presence of extracellular Ca2+ ions. We further describe the crystal structure of the RTX blocks IV-V of CyaA (CyaA1372-1681) that consists of a contiguous assembly of two β-rolls that differs substantially from the arrangement of the RTX blocks observed in RTX lipases or other RTX proteins. These results provide a novel structural insight into the architecture of the RTX domains of large RTX proteins and support the "push-ratchet" mechanism of the T1SS-mediated secretion of very large RTX proteins.
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Affiliation(s)
- Lucia Motlova
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Nela Klimova
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic.; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radovan Fiser
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic..
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152
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Oña Chuquimarca S, Ayala-Ruano S, Goossens J, Pauwels L, Goossens A, Leon-Reyes A, Ángel Méndez M. The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors. FRONTIERS IN PLANT SCIENCE 2020; 11:1139. [PMID: 32973821 PMCID: PMC7468482 DOI: 10.3389/fpls.2020.01139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/14/2020] [Indexed: 05/29/2023]
Abstract
The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant immunity. The increase in the concentration of JA leads to the decoupling of the JAZ repressor proteins and the bHLH transcription factor MYC3 causing the induction of genes of interest. The primary goal of this study was to identify the molecular basis of JAZ-MYC coupling. For this purpose, we modeled and validated 12 JAZ-MYC3 3D in silico structures and developed a molecular dynamics/machine learning pipeline to obtain two outcomes. First, we calculated the average free binding energy of JAZ-MYC3 complexes, which was predicted to be -10.94 +/-2.67 kJ/mol. Second, we predicted which ones should be the interface residues that make the predominant contribution to the free energy of binding (molecular hotspots). The predicted protein hotspots matched a conserved linear motif SL••FL•••R, which may have a crucial role during MYC3 recognition of JAZ proteins. As a proof of concept, we tested, both in silico and in vitro, the importance of this motif on PEAPOD (PPD) proteins, which also belong to the TIFY protein family, like the JAZ proteins, but cannot bind to MYC3. By mutating these proteins to match the SL••FL•••R motif, we could force PPDs to bind the MYC3 transcription factor. Taken together, modeling protein-protein interactions and using machine learning will help to find essential motifs and molecular mechanisms in the JA pathway.
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Affiliation(s)
- Samara Oña Chuquimarca
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sebastián Ayala-Ruano
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jonas Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Investigaciones Biológicas y Ambientales BIÓSFERA, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Miguel Ángel Méndez
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
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153
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Ginosyan S, Grabski H, Tiratsuyan S. In vitro and in silico Determination of the Interaction of Artemisinin with Human Serum Albumin. Mol Biol 2020. [DOI: 10.1134/s0026893320040056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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154
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Nguyen HL, Lan PD, Thai NQ, Nissley DA, O'Brien EP, Li MS. Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV? J Phys Chem B 2020; 124:7336-7347. [PMID: 32790406 PMCID: PMC7433338 DOI: 10.1021/acs.jpcb.0c04511] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The
2019 novel coronavirus (SARS-CoV-2) epidemic, which was first
reported in December 2019 in Wuhan, China, was declared a pandemic
by the World Health Organization in March 2020. Genetically, SARS-CoV-2
is closely related to SARS-CoV, which caused a global epidemic with
8096 confirmed cases in more than 25 countries from 2002 to 2003.
Given the significant morbidity and mortality rate, the current pandemic
poses a danger to all of humanity, prompting us to understand the
activity of SARS-CoV-2 at the atomic level. Experimental studies have
revealed that spike proteins of both SARS-CoV-2 and SARS-CoV bind
to angiotensin-converting enzyme 2 (ACE2) before entering the cell
for replication. However, the binding affinities reported by different
groups seem to contradict each other. Wrapp et al. (Science2020, 367, 1260–1263) showed
that the spike protein of SARS-CoV-2 binds to the ACE2 peptidase domain
(ACE2-PD) more strongly than does SARS-CoV, and this fact may be associated
with a greater severity of the new virus. However, Walls et al. (Cell2020, 181, 281–292)
reported that SARS-CoV-2 exhibits a higher binding affinity, but the
difference between the two variants is relatively small. To understand
the binding mechnism and experimental results, we investigated how
the receptor binding domain (RBD) of SARS-CoV (SARS-CoV-RBD) and SARS-CoV-2
(SARS-CoV-2-RBD) interacts with a human ACE2-PD using molecular modeling.
We applied a coarse-grained model to calculate the dissociation constant
and found that SARS-CoV-2 displays a 2-fold higher binding affinity.
Using steered all-atom molecular dynamics simulations, we demonstrate
that, like a coarse-grained simulation, SARS-CoV-2-RBD was associated
with ACE2-PD more strongly than was SARS-CoV-RBD, as evidenced by
a higher rupture force and larger pulling work. We show that the binding
affinity of both viruses to ACE2 is driven by electrostatic interactions.
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Affiliation(s)
- Hoang Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania 16802,United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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155
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Yadav S, Mandal H, Saravanan V, Das P, Singh SK. In vitro and in silico analysis of L. donovani enoyl acyl carrier protein reductase - A possible drug target. J Biomol Struct Dyn 2020; 39:6056-6069. [PMID: 32762412 DOI: 10.1080/07391102.2020.1802337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of increased resistance to the available drugs has created a situation that demands to find out more specific molecular drug targets for Leishmaniasis. The enoyl acyl carrier protein reductase (ENR), a regulatory enzyme in type II fatty acid synthesis, was confirmed as a novel drug target and triclosan as its specific inhibitor in many microorganisms. In this study, the triclosan was tested for the leishmanicidal property against Leishmania donovani (L. donovani) and the results of in vitro and ex vivo drug assays on promastigotes and amastigotes showed that triclosan possessed antileishmanial activity with a half minimal inhibitory concentration (IC50) of 30 µM. Consequently, adopting in silico approach, we have tested the triclosan's ability to bind with the L. donovani enoyl acyl carrier protein reductase (LdENR). The 3D structure of LdENR was modelled, triclosan and cofactors were docked in LdENR model and molecular dynamic simulations were performed to observe the protein-ligands interactions, stability, compactness and binding energy calculation of the ligands-LdENR complexes. The observation showed that triclosan stably interacted with LdENR in presence of both the cofactors (NADPH and NADH), however, simulation results favor NADH as a preferred co-factor for LdENR. These results support that the reduction of L. donovani growth in the in vitro and ex vivo drug assays may be due to the interaction of triclosan with LdENR, which should be confirmed through enzymatic assays. The results of this study suggest that LdENR could be a potential drug target and triclosan as a lead for Leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shalini Yadav
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
| | - Haraprasad Mandal
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India.,Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Vijayakumar Saravanan
- Division of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
| | - Pradeep Das
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), ICMR, Patna, India
| | - Shubhankar Kumar Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
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156
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Gyimesi G, Pujol-Giménez J, Kanai Y, Hediger MA. Sodium-coupled glucose transport, the SLC5 family, and therapeutically relevant inhibitors: from molecular discovery to clinical application. Pflugers Arch 2020; 472:1177-1206. [PMID: 32767111 PMCID: PMC7462921 DOI: 10.1007/s00424-020-02433-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023]
Abstract
Sodium glucose transporters (SGLTs) belong to the mammalian solute carrier family SLC5. This family includes 12 different members in human that mediate the transport of sugars, vitamins, amino acids, or smaller organic ions such as choline. The SLC5 family belongs to the sodium symporter family (SSS), which encompasses transporters from all kingdoms of life. It furthermore shares similarity to the structural fold of the APC (amino acid-polyamine-organocation) transporter family. Three decades after the first molecular identification of the intestinal Na+-glucose cotransporter SGLT1 by expression cloning, many new discoveries have evolved, from mechanistic analysis to molecular genetics, structural biology, drug discovery, and clinical applications. All of these advances have greatly influenced physiology and medicine. While SGLT1 is essential for fast absorption of glucose and galactose in the intestine, the expression of SGLT2 is largely confined to the early part of the kidney proximal tubules, where it reabsorbs the bulk part of filtered glucose. SGLT2 has been successfully exploited by the pharmaceutical industry to develop effective new drugs for the treatment of diabetic patients. These SGLT2 inhibitors, termed gliflozins, also exhibit favorable nephroprotective effects and likely also cardioprotective effects. In addition, given the recent finding that SGLT2 is also expressed in tumors of pancreas and prostate and in glioblastoma, this opens the door to potential new therapeutic strategies for cancer treatment by specifically targeting SGLT2. Likewise, further discoveries related to the functional association of other SGLTs of the SLC5 family to human pathologies will open the door to potential new therapeutic strategies. We furthermore hope that the herein summarized information about the physiological roles of SGLTs and the therapeutic benefits of the gliflozins will be useful for our readers to better understand the molecular basis of the beneficial effects of these inhibitors, also in the context of the tubuloglomerular feedback (TGF), and the renin-angiotensin system (RAS). The detailed mechanisms underlying the clinical benefits of SGLT2 inhibition by gliflozins still warrant further investigation that may serve as a basis for future drug development.
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Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, and Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Office D845, Freiburgstrasse 15, CH-3010, Bern, Switzerland.
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157
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Ahmad F, Shabaz Z, Azam SS. Insight into natural inhibitors and bridging docking to dynamic simulation against sugar Isomerase (SIS) domain protein. J Mol Model 2020; 26:221. [PMID: 32748070 DOI: 10.1007/s00894-020-04475-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022]
Abstract
The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain protein as an attractive receptor molecule for rational drug design. This protein is involved in lipopolysaccharide biosynthesis and catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. Molecular docking revealed compound 1 (2-(6-(N,N-dimethyl sulfamoyl)pipridin-4-yl)pyrazin-2-yl)imidazol-3-ium-1-ide) as the potent inhibitor having GOLD fitness score of 69. The complex is affirmed by half-site effect via simulation analysis. Complex stability was investigated via several approaches that follows dynamic simulation and binding energies. Trajectory analysis revealed slight change in ring positioning of inhibitor inside the active pocket during 130 ns (nanosecond). Interestingly, it was affirmed via binding interactions' density distribution. Hence, radial distribution function (RDF) inferred that SER55 and SER83 are the major residues that take part in hydrogen bonding and complex stability. Furthermore, an indigenously developed method axial frequency distribution (AFD) has revealed that ligand moved closer to the active site with both the residues SER55 and SER83 binding to the ligand. The phenomena was observed via rotating motion with respect to receptor center cavity. Thus, inhibitor movement towards allosteric site was observed at the end of simulations. Finally, binding free energy calculations by MMPB/GBSA predicts high compound affinity for the complex. Hence, findings from the current study will aid in the novel drug discovery and future experimental studies. Graphical abstract.
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Affiliation(s)
- Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Shabaz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
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158
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Characterization of cancer-related somatic mutations in the adenosine A2B receptor. Eur J Pharmacol 2020; 880:173126. [DOI: 10.1016/j.ejphar.2020.173126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/10/2023]
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159
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Medina E, Villalobos P, Hamilton GL, Komives EA, Sanabria H, Ramírez-Sarmiento CA, Babul J. Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. J Mol Biol 2020; 432:5411-5429. [PMID: 32735805 DOI: 10.1016/j.jmb.2020.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023]
Abstract
Forkhead box P (FoxP) proteins are unique transcription factors that spatiotemporally regulate gene expression by tethering two chromosome loci together via functional domain-swapped dimers formed through their DNA-binding domains. Further, the differential kinetics on this dimerization mechanism underlie an intricate gene regulation network at physiological conditions. Nonetheless, poor understanding of the structural dynamics and steps of the association process impedes to link the functional domain swapping to human-associated diseases. Here, we have characterized the DNA-binding domain of human FoxP1 by integrating single-molecule Förster resonance energy transfer and hydrogen-deuterium exchange mass spectrometry data with molecular dynamics simulations. Our results confirm the formation of a previously postulated domain-swapped (DS) FoxP1 dimer in solution and reveal the presence of highly populated, heterogeneous, and locally disordered dimeric intermediates along the dimer dissociation pathway. The unique features of FoxP1 provide a glimpse of how intrinsically disordered regions can facilitate domain swapping oligomerization and other tightly regulated association mechanisms relevant in biological processes.
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Affiliation(s)
- Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - George L Hamilton
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
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160
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Petrizzelli F, Biagini T, Barbieri A, Parca L, Panzironi N, Castellana S, Caputo V, Vescovi AL, Carella M, Mazza T. Mechanisms of pathogenesis of missense mutations on the KDM6A-H3 interaction in type 2 Kabuki Syndrome. Comput Struct Biotechnol J 2020; 18:2033-2042. [PMID: 32802275 PMCID: PMC7412721 DOI: 10.1016/j.csbj.2020.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
Mutations in genes encoding for histone methylation proteins are associated with several developmental disorders. Among them, KDM6A is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease. While nonsense mutations and short insertions/deletions are known to trigger pathogenic mechanisms, the functional effects of missense mutations are still uncharacterized. In this study, we demonstrate that a selected set of missense mutations significantly hamper the interaction between KDM6A and the histone H3, by modifying the dynamics of the linker domain, and then causing a loss of function effect.
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Affiliation(s)
- Francesco Petrizzelli
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Alessandro Barbieri
- School of Biology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Luca Parca
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Noemi Panzironi
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Angelo Luigi Vescovi
- IRCSS Casa Sollievo della Sofferenza, ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, San Giovanni Rotondo FG, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
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161
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Paul A, Srinivasan N. Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights. Proteins 2020; 88:1620-1638. [PMID: 32667690 DOI: 10.1002/prot.25981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/26/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022]
Abstract
Protein Kinase-Like Non-Kinases (PKLNKs), commonly known as "pseudokinases", are homologous to eukaryotic Ser/Thr/Tyr protein kinases (PKs) but lack the crucial aspartate residue in the catalytic loop, indispensable for phosphotransferase activity. Therefore, they are predicted to be "catalytically inactive" enzyme homologs. Analysis of protein-kinase like sequences from Arabidopsis thaliana led to the identification of more than 120 pseudokinases lacking catalytic aspartate, majority of which are closely related to the plant-specific receptor-like kinase family. These pseudokinases engage in different biological processes, enabled by their diverse domain architectures and specific subcellular localizations. Structural comparison of pseudokinases with active and inactive conformations of canonical PKs, belonging to both plant and animal origin, revealed unique structural differences. The currently available crystal structures of pseudokinases show that the loop topologically equivalent to activation segment of PKs adopts a distinct-folded conformation, packing against the pseudoenzyme core, in contrast to the extended and inhibitory geometries observed for active and inactive states, respectively, of catalytic PKs. Salt-bridge between ATP-binding Lys and DFG-Asp as well as hydrophobic interactions between the conserved nonpolar residue C-terminal to the equivalent DFG motif and nonpolar residues in C-helix mediate such a conformation in pseudokinases. This results in enhanced solvent accessibility of the pseudocatalytic loop in pseudokinases that can possibly serve as an interacting surface while associating with other proteins. Specifically, our analysis identified several residues that may be involved in pseudokinase regulation and hints at the repurposing of pseudocatalytic residues to achieve mechanistic control over noncatalytic functions of pseudoenzymes.
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Affiliation(s)
- Anindita Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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162
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Sánchez Di Maggio L, Tirloni L, Uhl M, Carmona C, Logullo C, Mulenga A, da Silva Vaz I, Berasain P. Serpins in Fasciola hepatica: insights into host-parasite interactions. Int J Parasitol 2020; 50:931-943. [PMID: 32668271 DOI: 10.1016/j.ijpara.2020.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 12/28/2022]
Abstract
Protease inhibitors play crucial roles in parasite development and survival, modulating the immune responses of their vertebrate hosts. Members of the serpin family are irreversible inhibitors of serine proteases and regulate systems related to defence against parasites. Limited information is currently available on protease inhibitors from the liver fluke Fasciola hepatica. In this study, we characterised four serpins from F. hepatica (FhS-1-FhS-4). Biochemical characterisation revealed that recombinant FhS-2 (rFhS) inhibits the activity of human neutrophil cathepsin G, while rFhS-4 inhibits the activity of bovine pancreatic chymotrypsin and cathepsin G. Consistent with inhibitor function profiling data, rFhS-4 inhibited cathepsin G-activated platelet aggregation in a dose-responsive manner.Similar to other serpins, rFhS2 and rFhS-4 bind to heparin with high affinity. Tissue localisation demonstrated that these serpins have different spatial distributions. FhS-2 is localised in the ovary, while FhS-4 was found in gut cells. Both of them co-localised in the spines within the tegument. These findings provide the basis for study of functional roles of these proteins as part of an immune evasion mechanism in the adult fluke, and in protection of eggs to ensure parasite life cycle continuity. Further understanding of serpins from the liver fluke may lead to the discovery of novel anti-parasitic interventions.
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Affiliation(s)
- Lucía Sánchez Di Maggio
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Lucas Tirloni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, USA
| | - Marcelle Uhl
- Laboratory of Chemistry and Function of Proteins and Peptides, Animal Experimentation Unit, Universidade Estadual do Norte Fluminence Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Carlos Carmona
- Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Carlos Logullo
- Laboratory of Chemistry and Function of Proteins and Peptides, Animal Experimentation Unit, Universidade Estadual do Norte Fluminence Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, USA
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Patrícia Berasain
- Unidad de Biología Parasitaria, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay.
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Long T, Alberich M, André F, Menez C, Prichard RK, Lespine A. The development of the dog heartworm is highly sensitive to sterols which activate the orthologue of the nuclear receptor DAF-12. Sci Rep 2020; 10:11207. [PMID: 32641726 PMCID: PMC7343802 DOI: 10.1038/s41598-020-67466-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/07/2020] [Indexed: 01/05/2023] Open
Abstract
Prevention therapy against Dirofilaria immitis in companion animals is currently threatened by the emergence of isolates resistant to macrocyclic lactone anthelmintics. Understanding the control over developmental processes in D. immitis is important for elucidating new approaches to heartworm control. The nuclear receptor DAF-12 plays a role in the entry and exit of dauer stage in Caenorhabditis elegans and in the development of free-living infective third-stage larvae (iL3) of some Clade IV and V parasitic nematodes. We identified a DAF-12 ortholog in the clade III nematode D. immitis and found that it exhibited a much higher affinity for dafachronic acids than described with other nematode DAF-12 investigated so far. We also modelled the DimDAF-12 structure and characterized the residues involved with DA binding. Moreover, we showed that cholesterol derivatives impacted the molting process from the iL3 to the fourth-stage larvae. Since D. immitis is unable to synthesize cholesterol and only completes its development upon host infection, we hypothesize that host environment contributes to its further molting inside the host vertebrate. Our discovery contributes to a better understanding of the developmental checkpoints of D. immitis and offers new perspectives for the development of novel therapies against filarial infections.
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Affiliation(s)
- Thavy Long
- INTHERES, Université de Toulouse, INRAE, ENVT, 31027, Toulouse Cedex 3, France.
- Institute of Parasitology, McGill University, Sainte-Anne-De-Bellevue, H9X3V9, QC, Canada.
| | - Mélanie Alberich
- INTHERES, Université de Toulouse, INRAE, ENVT, 31027, Toulouse Cedex 3, France
| | - François André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Cécile Menez
- INTHERES, Université de Toulouse, INRAE, ENVT, 31027, Toulouse Cedex 3, France
| | - Roger K Prichard
- Institute of Parasitology, McGill University, Sainte-Anne-De-Bellevue, H9X3V9, QC, Canada
| | - Anne Lespine
- INTHERES, Université de Toulouse, INRAE, ENVT, 31027, Toulouse Cedex 3, France.
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164
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Dhal AK, Pani A, Yun SI, Mahapatra RK. In-silico analysis of Calcium Dependent Protein Kinase 6 of Cr yptosporidium parvum through molecular modeling, docking, and dynamics simulation study. J Biomol Struct Dyn 2020; 39:5461-5470. [PMID: 32633680 DOI: 10.1080/07391102.2020.1790036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egress process during the infection of the host cells. The previous study reported that after the Calcium Dependent Protein Kinase 1 gene, Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum is expressed in all stages of the parasite (merozoites/schizonts as well as sexual stages) at a comparable level and makes it as a valid drug target. In this study, an attempt is made to address the similarity in sequences and phylogenetic study of Calcium Dependent Protein Kinase 6 (CDPK6) among Calcium Dependent Protein Kinases of Apicomplexans. Further, the three-dimensional structure determination of CDPK6 of C. parvum was performed through a molecular modeling approach followed by virtual screening of small-molecule inhibitors from different datasets. The best inhibitor from Tres Cantos Antimalarial Set with ID 11730 reported a binding affinity of -8.2 kcal/mol against CDPK6 of C. parvum. Furthermore, the reliability of the binding mode of the inhibitor is validated through a complex molecular dynamics simulation study for a time interval of 100 ns. The simulation study advocates that the inhibitor Tres Cantos Antimalarial Set_11730 formed a stable interaction with the predicted active site residues and can be considered for industrial pharmaceutical research in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
| | - Alok Pani
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, South Korea
| | - Soon-Il Yun
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, South Korea
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165
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Xu X, Zou X. MDockPeP: A Web Server for Blind Prediction of Protein-Peptide Complex Structures. Methods Mol Biol 2020; 2165:259-272. [PMID: 32621230 DOI: 10.1007/978-1-0716-0708-4_15] [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: 03/13/2023]
Abstract
Protein-peptide interactions mediate a wide range of important cellular tasks. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. Recently, we developed a docking-based method for predicting protein-peptide complex structures, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure. The produced modes are then evaluated with a statistical potential-based scoring function. The method has been implemented into an online server, MDockPeP server, which is freely available at http://zougrouptoolkit.missouri.edu/mdockpep . The server can be used for protein-peptide complex structure prediction. The server can also be used for initial-stage sampling of the protein-peptide binding modes for computational-demanding simulation or docking methods.
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Affiliation(s)
- Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA.,Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA. .,Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, USA. .,Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
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166
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Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, Zhang Z, Shu F, Huang W, Li Y, Zhang Z, Chen RA, Wu YJ, Peng SM, Huang M, Xie WJ, Cai QH, Hou FH, Chen W, Xiao L, Shen Y. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 2020; 583:286-289. [PMID: 32380510 DOI: 10.1101/2020.02.17.951335] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 05/21/2023]
Abstract
The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.
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Affiliation(s)
- Kangpeng Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Junqiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Niu Zhou
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xu Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jie-Jian Zou
- Guangdong Provincial Wildlife Rescue Center, Guangzhou, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaobing Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Fanfan Shu
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wanyi Huang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rui-Ai Chen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Wei-Jun Xie
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Fang-Hui Hou
- Guangdong Provincial Wildlife Rescue Center, Guangzhou, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China.
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Yongyi Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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Qin YG, Yang ZK, Song DL, Wang Q, Gu SH, Li WH, Duan HX, Zhou JJ, Yang XL. Bioactivities of synthetic salicylate-substituted carboxyl (E)-β-Farnesene derivatives as ecofriendly agrochemicals and their binding mechanism with potential targets in aphid olfactory system. PEST MANAGEMENT SCIENCE 2020; 76:2465-2472. [PMID: 32061021 DOI: 10.1002/ps.5787] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 01/31/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The aphid alarm pheromone, (E)-β-farnesene (EβF), is a natural product secreted from the aphid cornicle as a signal to warn companions of danger. Odorant binding proteins (OBPs) are the vital targets in insect signal transduction pathways. To improve bioactivity of EβF as more economic and stable aphid control agents, EβF derivatives containing an active substructure, salicylic acid moiety, were designed, synthesized, and evaluated for their bioactivities in a structure-function study under laboratory conditions. RESULTS EβF derivatives, (E)-3,7-dimethylocta-2,6-dien-1-yl-2-hydroxy-3-methylbenzoate and (E)-3,7-dimethylocta-2,6-dien-1-yl-2-hydroxy-3-methoxybenzoate showed outstanding aphid-repellent activity at a dose of 5 μg against Acyrthosiphon pisum (repellency proportions of 67.3% and 71.2%, respectively) and Myzus persicae (repellency proportions of 80.0% and 74.4%, respectively) in laboratory. EβF and most of its derivatives bound strongly to ApisOBP9 with a higher affinity than those of the reported potential targets AphisOBP3 and ApisOBP7. The binding affinities to these three ApisOBPs were generally consistent with the in vivo aphid-repellent activity. A molecular docking study suggested that the hydrophobic effect was crucial for the interactions between the derivatives and the OBPs. CONCLUSION New EβF derivatives containing salicylic acid moiety and their repellent activity, binding mechanism with three potential OBPs are presented. A new OBP, ApisOBP9, was characterized as a potential EβF and EβF derivatives binding protein for the first time. The hydrophobic nature of these analogues is responsible for their activity. Two analogues 3b and 3e with outstanding aphid-repellent activity could be new leads for aphid control agents.
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Affiliation(s)
- Yao-Guo Qin
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhao-Kai Yang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Dun-Lun Song
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qian Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shao-Hua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wen-Hao Li
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Hong-Xia Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Xin-Ling Yang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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168
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Site of Action of Brain Neurosteroid Pregnenolone Sulfate at the N-Methyl-D-Aspartate Receptor. J Neurosci 2020; 40:5922-5936. [PMID: 32611707 DOI: 10.1523/jneurosci.3010-19.2020] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
N-methyl-D-aspartate receptor (NMDAR) hypofunction has been implicated in several neurodevelopmental disorders. NMDAR function can be augmented by positive allosteric modulators, including endogenous compounds, such as cholesterol and neurosteroid pregnenolone sulfate (PES). Here we report that PES accesses the receptor via the membrane, and its binding site is different from that of cholesterol. Alanine mutagenesis has identified residues that disrupt the steroid potentiating effect at the rat GluN1 (G638; I642) and GluN2B (W559; M562; Y823; M824) subunit. Molecular dynamics simulation indicates that, in the absence of PES, the GluN2B M1 helix residue W559 interacts with the M4 helix residue M824. In the presence of PES, the M1 and M4 helices of agonist-activated receptor rearrange, forming a tighter interaction with the GluN1 M3 helix residues G638 and I642. This stabilizes the open-state position of the GluN1 M3 helices. Together, our data identify a likely binding site for the NMDAR-positive allosteric modulator PES and describe a novel molecular mechanism by which NMDAR activity can be augmented.SIGNIFICANCE STATEMENT There is considerable interest in drugs that enhance NMDAR function and could compensate for receptor hypofunction associated with certain neuropsychiatric disorders. Positive allosteric modulators of NMDARs include an endogenous neurosteroid pregnenolone sulfate (PES), but the binding site of PES on the NMDAR and the molecular mechanism of potentiation are unknown. We use patch-clamp electrophysiology in combination with mutagenesis and in silico modeling to describe the interaction of PES with the NMDAR. Our data indicate that PES binds to the transmembrane domain of the receptor at a discrete group of residues at the GluN2B membrane helices M1 and M4 and the GluN1 helix M3, and that PES potentiates NMDAR function by stabilizing the open-state position of the GluN1 M3 helices.
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169
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Mariano D, Pantuza N, Santos LH, Rocha REO, de Lima LHF, Bleicher L, de Melo-Minardi RC. Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. BMC Mol Cell Biol 2020; 21:50. [PMID: 32611314 PMCID: PMC7329481 DOI: 10.1186/s12860-020-00293-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 11/22/2022] Open
Abstract
Β-glucosidases are key enzymes used in second-generation biofuel production. They act in the last step of the lignocellulose saccharification, converting cellobiose in glucose. However, most of the β-glucosidases are inhibited by high glucose concentrations, which turns it a limiting step for industrial production. Thus, β-glucosidases have been targeted by several studies aiming to understand the mechanism of glucose tolerance, pH and thermal resistance for constructing more efficient enzymes. In this paper, we present a database of β-glucosidase structures, called Glutantβase. Our database includes 3842 GH1 β-glucosidase sequences collected from UniProt. We modeled the sequences by comparison and predicted important features in the 3D-structure of each enzyme. Glutantβase provides information about catalytic and conserved amino acids, residues of the coevolution network, protein secondary structure, and residues located in the channel that guides to the active site. We also analyzed the impact of beneficial mutations reported in the literature, predicted in analogous positions, for similar enzymes. We suggested these mutations based on six previously described mutants that showed high catalytic activity, glucose tolerance, or thermostability (A404V, E96K, H184F, H228T, L441F, and V174C). Then, we used molecular docking to verify the impact of the suggested mutations in the affinity of protein and ligands (substrate and product). Our results suggest that only mutations based on the H228T mutant can reduce the affinity for glucose (product) and increase affinity for cellobiose (substrate), which indicates an increment in the resistance to product inhibition and agrees with computational and experimental results previously reported in the literature. More resistant β-glucosidases are essential to saccharification in industrial applications. However, thermostable and glucose-tolerant β-glucosidases are rare, and their glucose tolerance mechanisms appear to be related to multiple and complex factors. We gather here, a set of information, and made predictions aiming to provide a tool for supporting the rational design of more efficient β-glucosidases. We hope that Glutantβase can help improve second-generation biofuel production. Glutantβase is available at http://bioinfo.dcc.ufmg.br/glutantbase .
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Affiliation(s)
- Diego Mariano
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Naiara Pantuza
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Lucianna H Santos
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rafael E O Rocha
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Leonardo H F de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Universidade Federal de São João Del-Rei, Campus Sete Lagoas, Sete Lagoas, 35701-970, Brazil
| | - Lucas Bleicher
- Protein Computational Biology Laboratory, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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170
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Molecular Topology of RNA Polymerase I Upstream Activation Factor. Mol Cell Biol 2020; 40:MCB.00056-20. [PMID: 32253346 DOI: 10.1128/mcb.00056-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Upstream activation factor (UAF) is a multifunctional transcription factor in Saccharomyces cerevisiae that plays dual roles in activating RNA polymerase I (Pol I) transcription and repression of Pol II. For Pol I, UAF binds to a specific upstream element in the ribosomal DNA (rDNA) promoter and interacts with two other Pol I initiation factors, the TATA-binding protein (TBP) and core factor (CF). We used an integrated combination of chemical cross-linking mass spectrometry (CXMS), molecular genetics, protein biochemistry, and structural modeling to understand the topological framework responsible for UAF complex formation. Here, we report the molecular topology of the UAF complex, describe new structural and functional domains that play roles in UAF complex integrity, assembly, and biological function, and provide roles for previously identified UAF domains that include the Rrn5 SANT and histone fold domains. We highlight the role of new domains in Uaf30 that include an N-terminal winged helix domain and a disordered tethering domain as well as a BORCS6-like domain found in Rrn9. Together, our results reveal a unique network of topological features that coalesce around a histone tetramer-like core to form the dual-function UAF complex.
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Veeravarapu H, Malkhed V, Mustyala KK, Vadija R, Malikanti R, Vuruputuri U, Muthyala MKK. Structure-based drug design, synthesis and screening of MmaA1 inhibitors as novel anti-TB agents. Mol Divers 2020; 25:351-366. [PMID: 32533514 DOI: 10.1007/s11030-020-10107-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/15/2020] [Indexed: 02/05/2023]
Abstract
Tuberculosis is one of the leading causes of death across the world. The treatment regimens for tuberculosis are well established, but still the control of the disease faces many challenges such as lengthy treatment protocols, drug resistance and toxicity. In the present work, mycolic acid methyl transferase (MmaA1), a protein involved in the maturation of mycolic acids in the biochemical pathway of the Mycobacterium, was studied for novel drug discovery. The homology model of the MmaA1 protein was built and validated by using computational techniques. The MmaA1 protein has 286 amino acid residues consisting of 10 α-helices and 7 β-sheets. The active site of the MmaA1 protein was identified using CASTp, SiteMap and PatchDock. Virtual screening studies were performed with two small molecule ligand databases: Asinex synergy and Diverse_Elite_Gold_Platinum databases having a total of 43,446 molecules and generated 1,30,814 conformers against the predicted and validated active site of the MmaA1 protein. Binding analysis showed that the residues ASP 19, PHE 22, TRP 30, TYR 32, TRP 74 and ALA 77 of MmaA1 protein have consistent interactions with the ligands. The hit ligands were further filtered by in silico ADME properties to eliminate potentially toxic molecules. Of the top 10 molecules, 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl) benzamide was synthesised and screened for in vitro anti-TB activity against Mtb H37Rv using MABA assay. The compound and its intermediates exhibited good in vitro anti-TB activity which can be taken up for future lead optimisation studies. Structure based virtual screening study was performed using a validated homology model against small molecules from two virtual compound libraries. Synthesised the lead compound 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl)benzamide obtained from virtual screening. In vitro activity against Mtb H37Rv has given a promising result.
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Affiliation(s)
- Hymavathi Veeravarapu
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India.,Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Vasavi Malkhed
- Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Kiran Kumar Mustyala
- Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Rajender Vadija
- Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Ramesh Malikanti
- Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Uma Vuruputuri
- Molecular Modelling Research Lab, Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana, India
| | - Murali Krishna Kumar Muthyala
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India.
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172
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Bafna D, Ban F, Rennie PS, Singh K, Cherkasov A. Computer-Aided Ligand Discovery for Estrogen Receptor Alpha. Int J Mol Sci 2020; 21:E4193. [PMID: 32545494 PMCID: PMC7352601 DOI: 10.3390/ijms21124193] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Breast cancer (BCa) is one of the most predominantly diagnosed cancers in women. Notably, 70% of BCa diagnoses are Estrogen Receptor α positive (ERα+) making it a critical therapeutic target. With that, the two subtypes of ER, ERα and ERβ, have contrasting effects on BCa cells. While ERα promotes cancerous activities, ERβ isoform exhibits inhibitory effects on the same. ER-directed small molecule drug discovery for BCa has provided the FDA approved drugs tamoxifen, toremifene, raloxifene and fulvestrant that all bind to the estrogen binding site of the receptor. These ER-directed inhibitors are non-selective in nature and may eventually induce resistance in BCa cells as well as increase the risk of endometrial cancer development. Thus, there is an urgent need to develop novel drugs with alternative ERα targeting mechanisms that can overcome the limitations of conventional anti-ERα therapies. Several functional sites on ERα, such as Activation Function-2 (AF2), DNA binding domain (DBD), and F-domain, have been recently considered as potential targets in the context of drug research and discovery. In this review, we summarize methods of computer-aided drug design (CADD) that have been employed to analyze and explore potential targetable sites on ERα, discuss recent advancement of ERα inhibitor development, and highlight the potential opportunities and challenges of future ERα-directed drug discovery.
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Affiliation(s)
| | | | | | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.B.); (F.B.); (P.S.R.); (K.S.)
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173
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Schwerd T, Krause F, Twigg SRF, Aschenbrenner D, Chen YH, Borgmeyer U, Müller M, Manrique S, Schumacher N, Wall SA, Jung J, Damm T, Glüer CC, Scheller J, Rose-John S, Jones EY, Laurence A, Wilkie AOM, Schmidt-Arras D, Uhlig HH. A variant in IL6ST with a selective IL-11 signaling defect in human and mouse. Bone Res 2020; 8:24. [PMID: 32566365 PMCID: PMC7289831 DOI: 10.1038/s41413-020-0098-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/11/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
The GP130 cytokine receptor subunit encoded by IL6ST is the shared receptor for ten cytokines of the IL-6 family. We describe a homozygous non-synonymous variant in IL6ST (p.R281Q) in a patient with craniosynostosis and retained deciduous teeth. We characterize the impact of the variant on cytokine signaling in vitro using transfected cell lines as well as primary patient-derived cells and support these findings using a mouse model with the corresponding genome-edited variant Il6st p.R279Q. We show that human GP130 p.R281Q is associated with selective loss of IL-11 signaling without affecting IL-6, IL-27, OSM, LIF, CT1, CLC, and CNTF signaling. In mice Il6st p.R279Q lowers litter size and causes facial synostosis and teeth abnormalities. The effect on IL-11 signaling caused by the GP130 variant shows incomplete penetrance but phenocopies aspects of IL11RA deficiency in humans and mice. Our data show that a genetic variant in a pleiotropic cytokine receptor can have remarkably selective defects.
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Affiliation(s)
- Tobias Schwerd
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Pediatrics, Dr von Hauner Children’s Hospital, LMU Munich, Munich, Germany
| | - Freia Krause
- Christian-Albrechts-University Kiel, Institute of Biochemistry, Kiel, Germany
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dominik Aschenbrenner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Yin-Huai Chen
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Uwe Borgmeyer
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Miryam Müller
- Christian-Albrechts-University Kiel, Institute of Biochemistry, Kiel, Germany
- Present Address: The Beatson Institute for Cancer Research, Glasgow, UK
| | - Santiago Manrique
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Neele Schumacher
- Christian-Albrechts-University Kiel, Institute of Biochemistry, Kiel, Germany
| | - Steven A. Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Jonathan Jung
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Present Address: School of Medicine, University of Glasgow, Glasgow, UK
| | - Timo Damm
- Section Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Claus-Christian Glüer
- Section Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Stefan Rose-John
- Christian-Albrechts-University Kiel, Institute of Biochemistry, Kiel, Germany
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Arian Laurence
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Dirk Schmidt-Arras
- Christian-Albrechts-University Kiel, Institute of Biochemistry, Kiel, Germany
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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174
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Aguayo-Ortiz R, Espinoza-Fonseca LM. Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities. Int J Mol Sci 2020; 21:ijms21114146. [PMID: 32532023 PMCID: PMC7313052 DOI: 10.3390/ijms21114146] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Sarcoendoplasmic reticulum calcium ATPase (SERCA), a member of the P-type ATPase family of ion and lipid pumps, is responsible for the active transport of Ca2+ from the cytoplasm into the sarcoplasmic reticulum lumen of muscle cells, into the endoplasmic reticulum (ER) of non-muscle cells. X-ray crystallography has proven to be an invaluable tool in understanding the structural changes of SERCA, and more than 70 SERCA crystal structures representing major biochemical states (defined by bound ligand) have been deposited in the Protein Data Bank. Consequently, SERCA is one of the best characterized components of the calcium transport machinery in the cell. Emerging approaches in the field, including spectroscopy and molecular simulation, now help integrate and interpret this rich structural information to understand the conformational transitions of SERCA that occur during activation, inhibition, and regulation. In this review, we provide an overview of the crystal structures of SERCA, focusing on identifying metrics that facilitate structure-based categorization of major steps along the catalytic cycle. We examine the integration of crystallographic data with different biophysical approaches and computational methods to link biochemical and structural states of SERCA that are populated in the cell. Finally, we discuss the challenges and new opportunities in the field, including structural elucidation of functionally important and novel regulatory complexes of SERCA, understanding the structural basis of functional divergence among homologous SERCA regulators, and bridging the gap between basic and translational research directed toward therapeutic modulation of SERCA.
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175
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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176
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Liu ZL, Hu JH, Jiang F, Wu YD. CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning. Bioinformatics 2020; 36:3385-3392. [PMID: 32215567 DOI: 10.1093/bioinformatics/btaa193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/06/2020] [Accepted: 03/22/2020] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION High-throughput sequencing discovers many naturally occurring disulfide-rich peptides or cystine-rich peptides (CRPs) with diversified bioactivities. However, their structure information, which is very important to peptide drug discovery, is still very limited. RESULTS We have developed a CRP-specific structure prediction method called Cystine-Rich peptide Structure Prediction (CRiSP), based on a customized template database with cystine-specific sequence alignment and three machine-learning predictors. The modeling accuracy is significantly better than several popular general-purpose structure modeling methods, and our CRiSP can provide useful model quality estimations. AVAILABILITY AND IMPLEMENTATION The CRiSP server is freely available on the website at http://wulab.com.cn/CRISP. CONTACT wuyd@pkusz.edu.cn or jiangfan@pku.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi-Lin Liu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jing-Hao Hu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,NanoAI Biotech Co., Ltd, Shenzhen 518118, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Shenzhen Bay Laboratory, Shenzhen 518055, China
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177
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A structurally minimized yet fully active insulin based on cone-snail venom insulin principles. Nat Struct Mol Biol 2020; 27:615-624. [PMID: 32483339 PMCID: PMC7374640 DOI: 10.1038/s41594-020-0430-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022]
Abstract
Human insulin and its current therapeutic analogs all show propensity, albeit varyingly, to self-associate into dimers and hexamers, which delays their onset of action and makes blood glucose management difficult for people with diabetes. Recently, we described a monomeric, insulin-like peptide in cone-snail venom with moderate human insulin-like bioactivity. Here, with insights from structural biology studies, we report the development of mini-Ins-a human des-octapeptide insulin analog-as a structurally minimal, full-potency insulin. Mini-Ins is monomeric and, despite the lack of the canonical B-chain C-terminal octapeptide, has similar receptor binding affinity to human insulin. Four mutations compensate for the lack of contacts normally made by the octapeptide. Mini-Ins also has similar in vitro insulin signaling and in vivo bioactivities to human insulin. The full bioactivity of mini-Ins demonstrates the dispensability of the PheB24-PheB25-TyrB26 aromatic triplet and opens a new direction for therapeutic insulin development.
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178
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Jafarpour R, Fatemi F, Eidi A, Mehrnejad F. Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2. J Biomol Struct Dyn 2020; 39:4122-4132. [PMID: 32462978 DOI: 10.1080/07391102.2020.1775119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the Acidithiobacillus ferrooxidans, and is the product of the rus gene expression. Herein, first the bacterial DNA of Acidithiobacillus sp. FJ2 was extracted. Then, the rus gene sequence and the sequence amino acid rusticyanin protein were determined. The Met148Leu mutation increased the oxidase activity of the rusticyanin protein, thereby enhancing the efficiency of the bioleaching process by bacteria Acidithiobacillus ferroxidans. Met148Leu mutation was created in the rusticyanin protein, then molecular dynamics (MD) simulations and structural analysis were performed. The MD analysis of the wild-type and mutant protein demonstrated a slight instability in the mutant protein and significant instability in the active site of the mutant protein. The usefulness of this study is the genetic manipulation of the native Acidithiobacillus sp. FJ2 bacterium, which can boost the bioleaching efficiency of the bacterium to some extent, and investigating its effects on the structure of a mutant protein using computational methods.
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Affiliation(s)
- Roghayeh Jafarpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Akram Eidi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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179
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Hijikata A, Shionyu-Mitsuyama C, Nakae S, Shionyu M, Ota M, Kanaya S, Shirai T. Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs. FEBS Lett 2020; 594:1960-1973. [PMID: 32379896 PMCID: PMC7267562 DOI: 10.1002/1873-3468.13806] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/28/2022]
Abstract
The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID‐19) caused by the novel coronavirus SARS‐CoV‐2 a pandemic. There is, however, no confirmed anti‐COVID‐19 therapeutic currently. In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Our theoretical models suggest several drugs, such as carfilzomib, sinefungin, tecadenoson, and trabodenoson, that could be further investigated for their potential for treating COVID‐19.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | | | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Japan
| | - Shigehiko Kanaya
- Computational Biology Laboratory, Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
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180
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In Silico Study and Optimization of Bacillus megaterium alpha-Amylases Production Obtained from Honey Sources. Curr Microbiol 2020; 77:2593-2601. [PMID: 32424606 DOI: 10.1007/s00284-020-02019-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
This study aimed to screen alpha-amylase producing microorganisms from honey as a low water activity medium, a suitable source for selecting stable and cost-beneficial bacterial enzyme production systems. Plackett-Burman method was used to select twelve effective factors including pH, inoculum size, temperature, time, corn starch, KH2PO4, peptone, MgSO4, CaCl2, NaCl, glycerin, and yeast extract concentrations on bacterial alpha-amylases production yield. The Box-Behnken method was utilized to optimize the level of selected significant factors. The stability of bacterial alpha-amylases was also determined in low pH and high-temperature conditions. In addition, in silico study was used to create the alpha-amylase structure and study the stability in high-temperature and low water available condition. Among all isolated and characterized microorganisms, Bacillus megaterium produced the highest amount of alpha-amylases. The in silico data showed the enzyme 3D structure similarity to alpha-amylase from Halothermothrix orenii and highly negative charge amino acids on its surface caused the enzyme activity and stability in low water conditions. Based on Box-Behnken results, the temperature 35 °C, pH 6 and starch 40 g/l were determined as the optimum level of significant factors to achieve the highest alpha-amylases unit (101.44 U/ml). This bacterial alpha-amylases enzyme showed stability at pH 5 and a range of temperatures from 40 to 60 °C that indicates this enzyme may possess the potential for using in industrial processes.
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181
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An Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase. Catalysts 2020. [DOI: 10.3390/catal10050555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The ribokinase superfamily catalyzes the phosphorylation of a vast diversity of substrates, and its members are characterized by the conservation of a common structural fold along with highly conserved sequence motifs responsible for phosphoryl transfer (GXGD) and stabilization of the metal-nucleotide complex (NXXE). Recently, a third motif (HXE) exclusive from ADP-dependent enzymes was identified, with its glutamic acid participating in water-mediated interactions with the metal-nucleotide complex and in stabilization of the ternary complex during catalysis. In this work, we bioinformatically determine that the aspartic acid of another motif (DPV), exclusively found in hydroxyethyl thiazole (THZK), hydroxymethyl pyrimidine (HMPK) and pyridoxal kinases (PLK), is structurally equivalent to the acidic residue in the HXE motif. Moreover, this residue is highly conserved among all ribokinase superfamily members. To determine whether the functional role of the DPV motif is similar to the HXE motif, we employed molecular dynamics simulations using crystal structures of phosphoryl donor substrate-complexed THZK and PLK, showing that its aspartic acid participated in water-mediated or direct interactions with the divalent metal of the metal-nucleotide complex. Lastly, enzyme kinetic assays on human PLK, an enzyme that utilizes zinc, showed that site-directed mutagenesis of the aspartic acid from the DPV motif abolishes the inhibition of this enzyme by increasing free zinc concentrations. Altogether, our results highlight that the DPV and HXE motifs are evolutionary markers of the functional and structural divergence of the ribokinase superfamily and evidence the role of the DPV motif in the interaction with both free and nucleotide-complexed divalent metals in the binding site of these enzymes.
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182
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Serçinoğlu O, Ozbek P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PLoS One 2020; 15:e0232849. [PMID: 32421728 PMCID: PMC7233585 DOI: 10.1371/journal.pone.0232849] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Faculty of Engineering, Fener, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Faculty of Engineering, Goztepe, Istanbul, Turkey
- * E-mail:
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183
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Salt Enhances the Thermostability of Enteroviruses by Stabilizing Capsid Protein Interfaces. J Virol 2020; 94:JVI.02176-19. [PMID: 32213614 DOI: 10.1128/jvi.02176-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/11/2020] [Indexed: 12/11/2022] Open
Abstract
Enteroviruses are common agents of infectious disease that are spread by the fecal-oral route. They are readily inactivated by mild heat, which causes the viral capsid to disintegrate or undergo conformational change. While beneficial for the thermal treatment of food or water, this heat sensitivity poses challenges for the stability of enterovirus vaccines. The thermostability of an enterovirus can be modulated by the composition of the suspending matrix, though the effects of the matrix on virus stability are not understood. Here, we determined the thermostability of four enterovirus strains in solutions with various concentrations of NaCl and different pH values. The experimental findings were combined with molecular modeling of the protein interaction forces at the pentamer and the protomer interfaces of the viral capsids. While pH only had a modest effect on thermostability, increasing NaCl concentrations raised the breakpoint temperatures of all viruses tested by up to 20°C. This breakpoint shift could be explained by an enhancement of the van der Waals attraction forces at the two protein interfaces. In comparison, the (net repulsive) electrostatic interactions were less affected by NaCl. Depending on the interface considered, the breakpoint temperature shifted by 7.5 or 5.6°C per 100-kcal/(mol·Å) increase in protein interaction force.IMPORTANCE The genus Enterovirus encompasses important contaminants of water and food (e.g., coxsackieviruses), as well as viruses of acute public health concern (e.g., poliovirus). Depending on the properties of the surrounding matrix, enteroviruses exhibit different sensitivities to heat, which in turn influences their persistence in the environment, during food treatment, and during vaccine storage. Here, we determined the effect of NaCl and pH on the heat stability of different enteroviruses and related the observed effects to changes in protein interaction forces in the viral capsid. We demonstrate that NaCl renders enteroviruses thermotolerant and that this effect stems from an increase in van der Waals forces at different protein subunits in the viral capsid. This work sheds light on the mechanism by which salt enhances virus stability.
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184
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Mohan V, Sullivan CS, Guo J, Wade SD, Majumder S, Agarwal A, Anton ES, Temple BS, Maness PF. Temporal Regulation of Dendritic Spines Through NrCAM-Semaphorin3F Receptor Signaling in Developing Cortical Pyramidal Neurons. Cereb Cortex 2020; 29:963-977. [PMID: 29415226 DOI: 10.1093/cercor/bhy004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 01/06/2018] [Indexed: 01/03/2023] Open
Abstract
Neuron-glial related cell adhesion molecule NrCAM is a newly identified negative regulator of spine density that genetically interacts with Semaphorin3F (Sema3F), and is implicated in autism spectrum disorders (ASD). To investigate a role for NrCAM in spine pruning during the critical adolescent period when networks are established, we generated novel conditional, inducible NrCAM mutant mice (Nex1Cre-ERT2: NrCAMflox/flox). We demonstrate that NrCAM functions cell autonomously during adolescence in pyramidal neurons to restrict spine density in the visual (V1) and medial frontal cortex (MFC). Guided by molecular modeling, we found that NrCAM promoted clustering of the Sema3F holoreceptor complex by interfacing with Neuropilin-2 (Npn2) and PDZ scaffold protein SAP102. NrCAM-induced receptor clustering stimulated the Rap-GAP activity of PlexinA3 (PlexA3) within the holoreceptor complex, which in turn, inhibited Rap1-GTPase and inactivated adhesive β1 integrins, essential for Sema3F-induced spine pruning. These results define a developmental function for NrCAM in Sema3F receptor signaling that limits dendritic spine density on cortical pyramidal neurons during adolescence.
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Affiliation(s)
- Vishwa Mohan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Chelsea S Sullivan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jiami Guo
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sarah D Wade
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Samarpan Majumder
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Amit Agarwal
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | - Eva S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Brenda S Temple
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Patricia F Maness
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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185
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Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, Zhang Z, Shu F, Huang W, Li Y, Zhang Z, Chen RA, Wu YJ, Peng SM, Huang M, Xie WJ, Cai QH, Hou FH, Chen W, Xiao L, Shen Y. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 2020; 583:286-289. [PMID: 32380510 DOI: 10.1038/s41586-020-2313-x] [Citation(s) in RCA: 460] [Impact Index Per Article: 115.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 11/09/2022]
Abstract
The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins-the most-trafficked mammal in the illegal wildlife trade-could represent a future threat to public health if wildlife trade is not effectively controlled.
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Affiliation(s)
- Kangpeng Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Junqiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Niu Zhou
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xu Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jie-Jian Zou
- Guangdong Provincial Wildlife Rescue Center, Guangzhou, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaobing Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Fanfan Shu
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wanyi Huang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rui-Ai Chen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Wei-Jun Xie
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China
| | - Fang-Hui Hou
- Guangdong Provincial Wildlife Rescue Center, Guangzhou, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, China.
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Yongyi Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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186
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Zhang GJ, Ma LF, Wang XQ, Zhou XG. Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1068-1081. [PMID: 30295627 DOI: 10.1109/tcbb.2018.2873691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ab initio protein tertiary structure prediction is one of the long-standing problems in structural bioinformatics. With the help of residue-residue contact and secondary structure prediction information, the accuracy of ab initio structure prediction can be enhanced. In this study, an improved differential evolution with secondary structure and residue-residue contact information referred to as SCDE is proposed for protein structure prediction. In SCDE, two score models based on secondary structure and contact information are proposed, and two selection strategies, namely, secondary structure-based selection strategy and contact-based selection strategy, are designed to guide conformation space search. A probability distribution function is designed to balance these two selection strategies. Experimental results on a benchmark dataset with 28 proteins and four free model targets in CASP12 demonstrate that the proposed SCDE is effective and efficient.
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187
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The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor. Viruses 2020; 12:v12050497. [PMID: 32365751 PMCID: PMC7291053 DOI: 10.3390/v12050497] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 disease has plagued over 200 countries with over three million cases and has resulted in over 200,000 deaths within 3 months. To gain insight into the high infection rate of the SARS-CoV-2 virus, we compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. SARS-CoV, SARS-CoV-2, and HCoV-NL63 recognize ACE2 as the natural receptor but present a distinct binding interface to ACE2 and a different network of residue–residue contacts. SARS-CoV and SARS-CoV-2 have comparable binding affinities achieved by balancing energetics and dynamics. The SARS-CoV-2–ACE2 complex contains a higher number of contacts, a larger interface area, and decreased interface residue fluctuations relative to the SARS-CoV–ACE2 complex. These findings expose an exceptional evolutionary exploration exerted by coronaviruses toward host recognition. We postulate that the versatility of cell receptor binding strategies has immediate implications for therapeutic strategies.
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188
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De Plano LM, Carnazza S, Franco D, Rizzo MG, Conoci S, Petralia S, Nicoletti A, Zappia M, Campolo M, Esposito E, Cuzzocrea S, Guglielmino SPP. Innovative IgG Biomarkers Based on Phage Display Microbial Amyloid Mimotope for State and Stage Diagnosis in Alzheimer's Disease. ACS Chem Neurosci 2020; 11:1013-1026. [PMID: 32176482 PMCID: PMC7997372 DOI: 10.1021/acschemneuro.9b00549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
![]()
An
innovative approach to identify new conformational antigens
of Aβ1–42 recognized by IgG autoantibodies
as biomarkers of state and stage in Alzheimer’s disease (AD)
patients is described. In particular, through the use of bioinformatics
modeling, conformational similarities between several Aβ1–42 forms and other amyloid-like proteins with F1 capsular
antigen (Caf1) of Yersinia pestis were first found.
pVIII M13 phage display libraries were then screened against YPF19,
anti-Caf1 monoclonal antibody, and IgGs of AD patients, in alternate
biopanning cycles of a so-called “double binding” selection.
From the selected phage clones, one, termed 12III1, was found to be
able to prevent in vitro Aβ1–42-induced cytotoxicity in SH-SY5Y cells, as well as to promote disaggregation
of preformed fibrils, to a greater extent with respect to wild-type
phage (pC89). IgG levels detected by 12III1 provided a significant
level of discrimination between diseased and nondemented subjects,
as well as a good correlation with the state progression of the disease.
These results give significant impact in AD state and stage diagnosis,
paving the way for the development not only for an innovative blood
diagnostic assay for AD precise diagnosis, progressive clinical assessment,
and screening but also for new effective treatments.
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Affiliation(s)
- Laura M. De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Santina Carnazza
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Domenico Franco
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Maria Giovanna Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Sabrina Conoci
- STmicroelectronics, Stradale Primosole, 50, 95121 Catania, Italy
- Distretto Tecnologico Micro e Nano Sistemi Sicilia, Strada VII-Zona Industriale, 95121 Catania, Italy
| | | | - Alessandra Nicoletti
- Neurology Clinic, Department “G.F. Ingrassia”, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123 Catania, Italy
| | - Mario Zappia
- Neurology Clinic, Department “G.F. Ingrassia”, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123 Catania, Italy
| | - Michela Campolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Salvatore P. P. Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
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189
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Großeholz R, Feldman-Salit A, Wanke F, Schulze S, Glöckner N, Kemmerling B, Harter K, Kummer U. Specifying the role of BAK1-interacting receptor-like kinase 3 in brassinosteroid signaling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:456-469. [PMID: 30912278 DOI: 10.1111/jipb.12803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/27/2019] [Indexed: 05/26/2023]
Abstract
Brassinosteroids (BR) are involved in the control of several developmental processes ranging from root elongation to senescence and adaptation to environmental cues. Thus, BR perception and signaling have to be precisely regulated. One regulator is BRI1-associated kinase 1 (BAK1)-interacting receptor-like kinase 3 (BIR3). In the absence of BR, BIR3 forms complexes with BR insensitive 1 (BRI1) and BAK1. However, the biophysical and energetic requirements for complex formation in the absence of the ligand have yet to be determined. Using computational modeling, we simulated the potential complexes between the cytoplasmic domains of BAK1, BRI1 and BIR3. Our calculations and experimental data confirm the interaction of BIR3 with BAK1 and BRI1, with the BAK1 BIR3 interaction clearly favored. Furthermore, we demonstrate that BIR3 and BRI1 share the same interaction site with BAK1. This suggests a competition between BIR3 and BRI1 for binding to BAK1, which results in preferential binding of BIR3 to BAK1 in the absence of the ligand thereby preventing the active participation of BAK1 in BR signaling. Our model also suggests that BAK1 and BRI1 can interact even while BAK1 is in complex with BIR3 at an additional binding site of BAK1 that does not allow active BR signaling.
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Affiliation(s)
- Ruth Großeholz
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Anna Feldman-Salit
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Sarina Schulze
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Nina Glöckner
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Birgit Kemmerling
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University Tübingen, 72076, Tübingen, Germany
| | - Ursula Kummer
- Centre for Organismal Studies/ BioQuant, Heidelberg University, 69120, Heidelberg, Germany
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190
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Lansky S, Salama R, Shulami S, Lavid N, Sen S, Schapiro I, Shoham Y, Shoham G. Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. J Mol Biol 2020; 432:2099-2120. [PMID: 32067952 DOI: 10.1016/j.jmb.2020.01.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Noa Lavid
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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191
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Hopkins JR, Crean RM, Catici DAM, Sewell AK, Arcus VL, Van der Kamp MW, Cole DK, Pudney CR. Peptide cargo tunes a network of correlated motions in human leucocyte antigens. FEBS J 2020; 287:3777-3793. [PMID: 32134551 PMCID: PMC8651013 DOI: 10.1111/febs.15278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Rory M Crean
- Department of Biology and Biochemistry, University of Bath, UK.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | | | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath, UK.,Centre for Therapeutic Innovation, University of Bath, UK
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192
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Xu J, Liu S, Liu G, Liu Y, He X. β-glucosidase from Hevea brasiliensis seeds: Purification, homology modeling, and insights into the substrate-binding model. J Food Biochem 2020; 44:e13206. [PMID: 32207174 DOI: 10.1111/jfbc.13206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 11/28/2022]
Abstract
The isolation of β-glucosidase from Hevea brasiliensis (Hbglu) seeds was investigated and a homology model was built on the MODELLER software to understand the structure feature. The quality of the model was evaluated on PROCHEK. The refined model was used for molecular docking on AutoDock 4.2 to determine the substrate- binding sites and potential substrates based on their calculated binding affinities. The substrate specificity of Hbglu was verified through the kinetic measurement of hydrolytic activities. Molecular dynamic simulations of cyanogenic β-glucosidase and ligand-bound complex showed that the free energy (ΔG) for the binding of p-nitrophenyl-β-D-glucopyranoside and daidzein-7-O-β-D-glucoside were -8.6 and -7.92 kcal/mol, respectively. Thus, daidzein-7-O-β-D-glucoside is a potential substrate. Future studies on the physicochemical properties and catalytic mechanisms will provide information on the molecular biological properties of Hbglu. PRACTICAL APPLICATIONS: This study reported the 3D structural simulation of β-glucosidase from Hbglu. The docking condition between Hbglu and various different substrates were assessed on Autodock. The results can be used as reference in designing enzymes, and improving the utilization of β-glucosidases for the hydrolysis of flavor precursors from fruits, teas, and wines and for the production of flavonoid compounds and cyanogenic glycoside degradation.
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Affiliation(s)
- Jiaqian Xu
- College of Food Science and Engineering, Hainan University, Hainan, China.,Engineering Research Center of Utilization of Tropical polysaccharide resources, Ministry of Education, Hainan, China
| | - Shisheng Liu
- College of Food Science and Engineering, Hainan University, Hainan, China.,Engineering Research Center of Utilization of Tropical polysaccharide resources, Ministry of Education, Hainan, China
| | - Gang Liu
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Yu Liu
- Engineering Research Center of Utilization of Tropical polysaccharide resources, Ministry of Education, Hainan, China
| | - Xu He
- Engineering Research Center of Utilization of Tropical polysaccharide resources, Ministry of Education, Hainan, China
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193
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Yao J, He Y, Su N, Bharath SR, Tao Y, Jin JM, Chen W, Song H, Tang SY. Developing a highly efficient hydroxytyrosol whole-cell catalyst by de-bottlenecking rate-limiting steps. Nat Commun 2020; 11:1515. [PMID: 32251291 PMCID: PMC7090077 DOI: 10.1038/s41467-020-14918-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
Hydroxytyrosol is an antioxidant free radical scavenger that is biosynthesized from tyrosine. In metabolic engineering efforts, the use of the mouse tyrosine hydroxylase limits its production. Here, we design an efficient whole-cell catalyst of hydroxytyrosol in Escherichia coli by de-bottlenecking two rate-limiting enzymatic steps. First, we replace the mouse tyrosine hydroxylase by an engineered two-component flavin-dependent monooxygenase HpaBC of E. coli through structure-guided modeling and directed evolution. Next, we elucidate the structure of the Corynebacterium glutamicum VanR regulatory protein complexed with its inducer vanillic acid. By switching its induction specificity from vanillic acid to hydroxytyrosol, VanR is engineered into a hydroxytyrosol biosensor. Then, with this biosensor, we use in vivo-directed evolution to optimize the activity of tyramine oxidase (TYO), the second rate-limiting enzyme in hydroxytyrosol biosynthesis. The final strain reaches a 95% conversion rate of tyrosine. This study demonstrates the effectiveness of sequentially de-bottlenecking rate-limiting steps for whole-cell catalyst development. Whole-cell catalyst-based hydroxytyrosol production is low. Here, the authors increase the efficiency of its production in E. coli by de-bottlenecking two enzymatic steps catalyzed by monooxygenase and tyramine oxidase using structure-based enzyme redesign or in vivo-directed evolution with the aid of a newly developed biosensor.
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Affiliation(s)
- Jun Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yang He
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore
| | - Nannan Su
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore
| | | | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China.
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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194
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Boldrini-França J, Pinheiro-Junior EL, Peigneur S, Pucca MB, Cerni FA, Borges RJ, Costa TR, Carone SEI, Fontes MRDM, Sampaio SV, Arantes EC, Tytgat J. Beyond hemostasis: a snake venom serine protease with potassium channel blocking and potential antitumor activities. Sci Rep 2020; 10:4476. [PMID: 32161292 PMCID: PMC7066243 DOI: 10.1038/s41598-020-61258-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Snake venom serine proteases (SVSPs) are complex and multifunctional enzymes, acting primarily on hemostasis. In this work, we report the hitherto unknown inhibitory effect of a SVSP, named collinein-1, isolated from the venom of Crotalus durissus collilineatus, on a cancer-relevant voltage-gated potassium channel (hEAG1). Among 12 voltage-gated ion channels tested, collinein-1 selectively inhibited hEAG1 currents, with a mechanism independent of its enzymatic activity. Corroboratively, we demonstrated that collinein-1 reduced the viability of human breast cancer cell line MCF7 (high expression of hEAG1), but does not affect the liver carcinoma and the non-tumorigenic epithelial breast cell lines (HepG2 and MCF10A, respectively), which present low expression of hEAG1. In order to obtain both functional and structural validation of this unexpected discovery, where an unusually large ligand acts as an inhibitor of an ion channel, a recombinant and catalytically inactive mutant of collinein-1 (His43Arg) was produced and found to preserve its capability to inhibit hEAG1. A molecular docking model was proposed in which Arg79 of the SVSP 99-loop interacts directly with the potassium selectivity filter of the hEAG1 channel.
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Affiliation(s)
- Johara Boldrini-França
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil.,University of Vila Velha, Av. Comissário José Dantas de Melo, 21, Boa Vista II, 29102-920, Vila Velha, ES, Brazil
| | - Ernesto Lopes Pinheiro-Junior
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil.,Toxicology and Pharmacology, KU Leuven, O&N II Herestraat 49, PO 922, 3000, Leuven, Belgium
| | - Steve Peigneur
- Toxicology and Pharmacology, KU Leuven, O&N II Herestraat 49, PO 922, 3000, Leuven, Belgium
| | - Manuela Berto Pucca
- Medical School of Roraima, Federal University of Roraima, Av. Capitão Ene Garcez, 2413, Bairro Aeroporto, 69310-970, Boa Vista, RR, Brazil
| | - Felipe Augusto Cerni
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil
| | - Rafael Junqueira Borges
- Institute of Biosciences, São Paulo State University (UNESP), Rua Prof. Dr. Antonio Celso Wagner Zanin, 250, 18618-689, Botucatu, SP, Brazil
| | - Tássia Rafaella Costa
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil
| | - Sante Emmanuel Imai Carone
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil
| | - Marcos Roberto de Mattos Fontes
- Institute of Biosciences, São Paulo State University (UNESP), Rua Prof. Dr. Antonio Celso Wagner Zanin, 250, 18618-689, Botucatu, SP, Brazil
| | - Suely Vilela Sampaio
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil
| | - Eliane Candiani Arantes
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, 14040-903, Ribeirão Preto, SP, Brazil.
| | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, O&N II Herestraat 49, PO 922, 3000, Leuven, Belgium.
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195
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Exploring the binding mode of triflamide derivatives at the active site of Topo I and Topo II enzymes: In silico analysis and precise molecular docking. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-1750-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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196
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Naresh GKRS, Guruprasad L. Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases. J Biomol Struct Dyn 2020; 39:1213-1235. [PMID: 32070235 DOI: 10.1080/07391102.2020.1730968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Receptor tyrosine kinases (RTKs) are essential proteins in the regulation of cell signaling. Tyro3, Axl and Mer are members of TAM RTKs and are overexpressed in several cancer forms. Kinase inhibitors such as cabozantinib, foretinib are reported to inhibit TAM kinases at nanomolar concentrations. The atomistic details of structure and mechanism of functional regulation is required to understand their normal physiological process and when bound to an inhibitor. The docking of cabozantinib into the active state conformations of TAM kinases (crystal structure and computational models) revealed the best binding pose and the complex formation that is mediated through non-bonding interactions involving the hinge region residues. The alterations in the conformations and the regions of flexibility in apo and complexed TAM kinases as a course of time are studied using 250 ns molecular dynamics (MD) simulations. The post-MD trajectory analysis using Python libraries like ProDy, MDTraj and PyEMMA revealed encrypted protein dynamic motions in active kinetic metastable states. Comparison between Principal component analysis and Anisotropic mode analysis deciphered structural residue interactions and salt bridge contacts between apo and inhibitor bound TAM kinases. Various structural changes occurred in αC-helix and activation loop involving hydrogen bonding between residues from Lys-(β3 sheet), Glu-(αC-helix) and Asp-(DFG-motif) resulting in higher RMSD. Mechanical stiffness plots revealed that similar regions in apo and cabozantinib bound Axl fluctuated during MD simulations whereas different regions in Tyro3 and Mer kinases. The residue interaction network plots revealed important salt bridges that lead to constrained domain motions in the TAM kinases.Communicated by Ramaswamy H. Sarma.
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197
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Identification of a novel biallelic missense variant in the KIAA0825 underlies postaxial polydactyly type A. Genomics 2020; 112:2729-2733. [PMID: 32147526 DOI: 10.1016/j.ygeno.2020.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/01/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023]
Abstract
Postaxial polydactyly (PAP) is characterized by development of extra digits, which mostly segregates in autosomal recessive pattern. The underlying genetic cause of recessive non-syndromic PAP type A has been associated with sequence variants in five different genes (ZNF141, IQCE, GLI1, FAM92A, KIAA0825). The present study was aimed to investigate clinical and genetic causes of PAPA in a consanguineous family of Pakistani origin. Microsatellite-based linkage analysis was used to search for the disease-causing gene. Linkage in the family was established at chromosome 5q15 harbouring a candidate gene KIAA0825. Subsequently, Sanger sequencing revealed a novel homozygous missense variant [c.50T>C; p. (Leu17Ser)] in the gene, which co-segregated with the disease within the family. Protein structural analysis predicted a substantial change in the secondary structure of the mutant protein affecting its function. This is the third disease causing variant identified in the KIAA0825. This has not only expanded spectrum of the mutations in the gene but also further substantiated its role in the limb development in human.
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198
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In-silico and in-vitro analysis of endocan interaction with statins. Int J Biol Macromol 2020; 146:1087-1099. [DOI: 10.1016/j.ijbiomac.2019.09.235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 01/11/2023]
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199
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Lima LHFD, Fernandez-Quintéro ML, Rocha REO, Mariano DCB, de Melo-Minardi RC, Liedl KR. Conformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases - a computational study. J Biomol Struct Dyn 2020; 39:1621-1634. [PMID: 32107974 DOI: 10.1080/07391102.2020.1734484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
β-glucosidases (EC 3.2.1.21) have been described as essential to second-generation biofuel production. They act in the last step of the lignocellulosic saccharification, cleaving the β - 1,4 glycosidic bonds in cellobiose to produce two molecules of glucose. However, β-glucosidases have been described as strongly inhibited by glucose, causing an increment of cellobiose concentration. Also, cellobiose is an inhibitor of other enzymes used in this process, such as exoglucanases and endoglucanases. Hence, the engineering of thermostable and glucose-tolerant β-glucosidases has been targeted by many studies. In this study, we performed high sampling accelerated molecular dynamics for a wild glucose-tolerant GH1 β-glucosidase (Bgl1A), a wild non-tolerant (Bgl1B), and a set of glucose-tolerant Bgl1B's mutants: V302F, N301Q/V302F, F172I, V227M, G246S, T299S, and H228T. Our results suggest that point mutations promissory to induce glucose tolerance trend to enhance the mobility of the flexible loops around the active site. Mutations affected B and C loops regions, and an αβ-hairpin motif between them. Conformational clusters and free energy landscape profiles suggest that the mobility acquired by mutants allows a higher closure of the substrate channel. This closure is compatible with a higher impedance for glucose entrance and stimulus of its withdrawal. Based on mutants' structural analyses, we inferred that both the direct stereochemical effect on the glucose path and the changes in the mobility affect glucose tolerance. We hope these results be useful for the rational design of glucose-tolerant and industrially promising enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Leonardo Henrique Franca de Lima
- Laboratory of Molecular Modeling and Bioinformatics, Department of Exact and Biological Sciences (DECEB), Universidade Federal de São João Del-Rei, Sete Lagoas, Brazil
| | - Monica Lisa Fernandez-Quintéro
- Institute of General, Inorganic and Theoretical Chemistry (IGITC), Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens-Universität-Innsbruck, Innsbruck, Austria
| | - Rafael Eduardo Oliveira Rocha
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Klaus Roman Liedl
- Institute of General, Inorganic and Theoretical Chemistry (IGITC), Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens-Universität-Innsbruck, Innsbruck, Austria
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200
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Mukherjee M, Gupta A, Sankararamakrishnan R. Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study. Biophys J 2020; 118:846-860. [PMID: 31968229 DOI: 10.1016/j.bpj.2019.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022] Open
Abstract
Formate/nitrite transporters (FNTs) selectively transport monovalent anions and are found in prokaryotes and lower eukaryotes. They play a significant role in bacterial growth and act against the defense mechanism of infected hosts. Because FNTs do not occur in higher animals, they are attractive drug targets for many bacterial diseases. Phylogenetic analysis revealed that they can be classified into eight subgroups, two of which belong to the uncharacterized YfdC-α and YfdC-β groups. Experimentally determined structures of FNTs belonging to different phylogenetic groups adopt the unique aquaporin-like hourglass helical fold. We considered the formate channel from Vibrio cholerae, the hydrosulphide channel from Clostridium difficile, and the uncharacterized channel from Escherichia coli (EcYfdC) to investigate the mechanism of transport and selectivity. Using equilibrium molecular dynamics and umbrella sampling studies, we determined temporal channel radius profiles, permeation events, and potential of mean force profiles of different substrates with the conserved central histidine residue in protonated or neutral form. Unlike the formate channel from V. cholerae and the hydrosulphide channel from C. difficile, molecular dynamics studies showed that the formate substrate was unable to enter the vestibule region of EcYfdC. Absence of a conserved basic residue and presence of acidic residues in the vestibule regions, conserved only in YfdC-α, were found to be responsible for high energy barriers for the anions to enter EcYfdC. Potential of mean force profiles generated for ammonia and ammonium ion revealed that EcYfdC can transport neutral solutes and could possibly be involved in the transport of cations analogous to the mechanism proposed for ammonium transporters. Although YfdC members belong to the FNT family, our studies strongly suggest that EcYfdC is not an anion channel. Absence or presence of specific charged residues at particular positions makes EcYfdC selective for neutral or possibly cationic substrates. Further experimental studies are needed to get a definitive answer to the question of the substrate selectivity of EcYfdC. This provides an example of membrane proteins from the same family transporting substrates of different chemical nature.
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Affiliation(s)
- Mishtu Mukherjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ankita Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
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