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Chen C, Zhu T, Liu X, Zhu D, Zhang Y, Wu S, Han C, Zhang H, Luo J, Kong L. Identification of a novel PHGDH covalent inhibitor by chemical proteomics and phenotypic profiling. Acta Pharm Sin B 2022; 12:246-261. [PMID: 35127383 PMCID: PMC8799887 DOI: 10.1016/j.apsb.2021.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
The first rate-limiting enzyme of the serine synthesis pathway (SSP), phosphoglycerate dehydrogenase (PHGDH), is hyperactive in multiple tumors, which leads to the activation of SSP and promotes tumorigenesis. However, only a few inhibitors of PHGDH have been discovered to date, especially the covalent inhibitors of PHGDH. Here, we identified withangulatin A (WA), a natural small molecule, as a novel covalent inhibitor of PHGDH. Affinity-based protein profiling identified that WA could directly bind to PHGDH and inactivate the enzyme activity of PHGDH. Biolayer interferometry and LC-MS/MS analysis further demonstrated the selective covalent binding of WA to the cysteine 295 residue (Cys295) of PHGDH. With the covalent modification of Cys295, WA blocked the substrate-binding domain (SBD) of PHGDH and exerted an allosteric effect to induce PHGDH inactivation. Further studies revealed that with the inhibition of PHGDH mediated by WA, the glutathione synthesis was decreased and intracellular levels of reactive oxygen species (ROS) were elevated, leading to the inhibition of tumor proliferation. This study indicates WA as a novel PHGDH covalent inhibitor, which identifies Cys295 as a novel allosteric regulatory site of PHGDH and holds great potential in developing anti-tumor agents for targeting PHGDH.
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Key Words
- 3-PG, 3-phosphoglycerate
- 3-PHP, 3-phosphohydroxypyruvate
- ABPP, affinity-based protein profiling
- BLI, biolayer interferometry assay
- CETSA, cellular thermal shift assay
- Chemical proteomics
- Colon cancer
- Covalent inhibitor
- CuAAC, copper-catalyzed alkyne–azide cycloaddition
- DARTS, drug affinity responsive target stability
- GSH, glutathione
- MD, molecular dynamics
- NADPH, nicotinamide adenine dinucleotide phosphate
- Oxidative stress
- PHGDH, phosphoglycerate dehydrogenase
- PSAT, phosphoserine aminotransferase
- Phosphoglycerate dehydrogenase
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- ROS, reactive oxygen species
- SBD, substrate-binding domain
- SSP, serine synthesis pathway
- Serine synthesis pathway
- TBTA, tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine
- TCEP, tris(2-carboxyethyl) phosphine
- Withangulatin A
- Withanolides
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianguang Luo
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
| | - Lingyi Kong
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
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Calligari P, Santucci V, Stella L, Bocchinfuso G. Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state. Comput Struct Biotechnol J 2021; 19:6125-6139. [PMID: 34900129 PMCID: PMC8632847 DOI: 10.1016/j.csbj.2021.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/31/2021] [Accepted: 10/31/2021] [Indexed: 11/07/2022] Open
Abstract
The Src-homology 2 domain containing phosphatase 2 (SHP2) plays a critical role in crucial signaling pathways and is involved in oncogenesis and in developmental disorders. Its structure includes two SH2 domains (N-SH2 and C-SH2), and a protein tyrosine phosphatase (PTP) domain. Under basal conditions, SHP2 is auto-inhibited, with the N-SH2 domain blocking the PTP active site. Activation involves a rearrangement of the domains that makes the catalytic site accessible, coupled to the association between the SH2 domains and cognate proteins containing phosphotyrosines. Several aspects of this transition are debated and competing mechanistic models have been proposed. A crystallographic structure of SHP2 in an active state has been reported (PDB code 6crf), but several lines of evidence suggests that it is not fully representative of the conformations populated in solution. To clarify the structural rearrangements involved in SHP2 activation, enhanced sampling simulations of the autoinhibited and active states have been performed, for wild type SHP2 and its pathogenic E76K variant. Our results demonstrate that the crystallographic conformation of the active state is unstable in solution, and multiple interdomain arrangements are populated, thus allowing association to bisphosphorylated sequences. Contrary to a recent proposal, activation is coupled to the conformational changes of the N-SH2 binding site, which is significantly more accessible in the active sate, rather than to the structure of the central β-sheet of the domain. In this coupling, a previously undescribed role for the N-SH2 BG loop emerged.
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Key Words
- BTLA, B and T lymphocyte attenuator
- CTLA-4, cytotoxic T lymphocyte-associated antigen 4
- FRET, Förster resonance energy transfer
- Inter-domain dynamics
- JMML, juvenile myelomonocytic leukemia
- MD, molecular dynamics
- NS, Noonan syndrome
- NSML, Noonan syndrome with multiple lentigines
- PD-1, programmed cell death protein 1
- PDB, protein data bank
- PMF, potential of mean force
- PTP, protein tyrosine phosphatase
- Protein flexibility
- REMD, replica exchange molecular dynamics
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- RTK, receptor tyrosine kinase
- Replica exchange molecular dynamics simulations
- SASA, solvent accessible surface area
- SAXS, small angle X-ray scattering
- SH2, Src homology 2
- SHP2 regulatory mechanism
- SHP2, Src homology 2 domain-containing phosphatase 2
- SIRPalpha, signal regulatory protein alpha
- pY, phosphorylated tyrosine
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Affiliation(s)
- Paolo Calligari
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Valerio Santucci
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
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Ahmad Mir S, Firoz A, Alaidarous M, Alshehri B, Aziz Bin Dukhyil A, Banawas S, Alsagaby SA, Alturaiki W, Ahmad Bhat G, Kashoo F, Abdel-Hadi AM. Identification of SARS-CoV-2 RNA-dependent RNA polymerase inhibitors from the major phytochemicals of Nigella sativa: An in silico approach. Saudi J Biol Sci 2021; 29:394-401. [PMID: 34518755 PMCID: PMC8426002 DOI: 10.1016/j.sjbs.2021.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19), which emerged in December 2019, continues to be a serious health concern worldwide. There is an urgent need to develop effective drugs and vaccines to control the spread of this disease. In the current study, the main phytochemical compounds of Nigella sativa were screened for their binding affinity for the active site of the RNA-dependent RNA polymerase (RdRp) enzyme of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The binding affinity was investigated using molecular docking methods, and the interaction of phytochemicals with the RdRp active site was analyzed and visualized using suitable software. Out of the nine phytochemicals of N. sativa screened in this study, a significant docking score was observed for four compounds, namely α-hederin, dithymoquinone, nigellicine, and nigellidine. Based on the findings of our study, we report that α-hederin, which was found to possess the lowest binding energy (–8.6 kcal/mol) and hence the best binding affinity, is the best inhibitor of RdRp of SARS-CoV-2, among all the compounds screened here. Our results prove that the top four potential phytochemical molecules of N. sativa, especially α-hederin, could be considered for ongoing drug development strategies against SARS-CoV-2. However, further in vitro and in vivo testing are required to confirm the findings of this study.
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Affiliation(s)
- Shabir Ahmad Mir
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Ahmad Firoz
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Ssaudi Arabia
| | - Mohammed Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Abdul Aziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia.,Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Suliman A Alsagaby
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Gulzar Ahmad Bhat
- Department of Clinical Biochemistry, Sher-i-Kashmir Institute of Medical Science, Srinagar, India
| | - Faizan Kashoo
- Department of Physical Therapy and Health Rehabilitation, College of Applied Medical Sciences, Majmaah University, Al Majmaah-11952, Saudi Arabia
| | - Ahmad M Abdel-Hadi
- Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi Arabia
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Remya C, Dileep KV, Koti Reddy E, Mantosh K, Lakshmi K, Sarah Jacob R, Sajith AM, Jayadevi Variyar E, Anwar S, Zhang KYJ, Sadasivan C, Omkumar RV. Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase - Design, synthesis and biological evaluation. Comput Struct Biotechnol J 2021; 19:4517-4537. [PMID: 34471497 PMCID: PMC8379669 DOI: 10.1016/j.csbj.2021.07.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
The complex and multifactorial nature of neuropsychiatric diseases demands multi-target drugs that can intervene with various sub-pathologies underlying disease progression. Targeting the impairments in cholinergic and glutamatergic neurotransmissions with small molecules has been suggested as one of the potential disease-modifying approaches for Alzheimer’s disease (AD). Tacrine, a potent inhibitor of acetylcholinesterase (AChE) is the first FDA approved drug for the treatment of AD. Tacrine is also a low affinity antagonist of N-methyl-D-aspartate receptor (NMDAR). However, tacrine was withdrawn from its clinical use later due to its hepatotoxicity. With an aim to develop novel high affinity multi-target directed ligands (MTDLs) against AChE and NMDAR, with reduced hepatotoxicity, we performed in silico structure-based modifications on tacrine, chemical synthesis of the derivatives and in vitro validation of their activities. Nineteen such derivatives showed inhibition with IC50 values in the range of 18.53 ± 2.09 – 184.09 ± 19.23 nM against AChE and 0.27 ± 0.05 – 38.84 ± 9.64 μM against NMDAR. Some of the selected compounds also protected rat primary cortical neurons from glutamate induced excitotoxicity. Two of the tacrine derived MTDLs, 201 and 208 exhibited in vivo efficacy in rats by protecting against behavioral impairment induced by administration of the excitotoxic agent, monosodium glutamate. Additionally, several of these synthesized compounds also exhibited promising inhibitory activitiy against butyrylcholinesterase. MTDL-201 was also devoid of hepatotoxicity in vivo. Given the therapeutic potential of MTDLs in disease-modifying therapy, our studies revealed several promising MTDLs among which 201 appears to be a potential candidate for immediate preclinical evaluations.
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Key Words
- AChE, acetylcholinesterase
- AChEIs, acetylcholinesterase inhibitors
- AChT, acetylthiocholine
- AD, Alzheimer’s disease
- ADME, absorption, distribution, metabolism and excretion
- Acetylcholinesterase
- Alzheimer’s disease
- BBB, blood brain barrier
- Ca2+, calcium
- ChE, Cholinesterases
- DMEM, Dulbecco’s modified Eagle’s medium
- DTNB, 5,5-dithiobis-(2-nitrobenzoic acid)
- ENM, elastic network modeling
- ER, endoplasmic reticulum
- FRET, fluorescence resonance energy transfer
- G6PD, glucose-6-phosphate dehydrogenase
- HBSS, Hank's balanced salt solution
- IP, intraperitoneal
- LBD, Ligand binding domain
- LC-MS, Liquid chromatography-mass spectrometry
- LiCABEDS, Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps
- MAP2, microtubule associated protein 2
- MD, Molecular dynamics
- MTDLs
- MTDLs, multi-target directed ligands
- MWM, Morris water maze
- NBM, neurobasal medium
- NMA, normal mode analysis
- NMDA receptor
- NMDAR, N-methyl-D-aspartate receptor
- Neuroprotection
- OPLS, Optimized potential for liquid simulations
- PBS, phosphate-buffered saline
- PFA, paraformaldehyde
- Polypharmacology
- RMSD, root mean square deviation
- SAR, structure-activity relationships
- SD, standard deviation
- SVM, support vector machine
- Structure-based drug design
- TBI, traumatic brain injury
- TMD, transmembrane domain
- Tacrine
- h-NMDAR, human NMDAR
- hAChE, human AChE
- ppm, parts per million
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Affiliation(s)
- Chandran Remya
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - K V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Computational and Structural Biology, Jubilee Center for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala 680005, India
| | - Eeda Koti Reddy
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kumar Mantosh
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Kesavan Lakshmi
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Reena Sarah Jacob
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Ayyiliyath M Sajith
- Post Graduate and Research Department of Chemistry, Kasargod Govt. College, Kannur University, Kasaragod, India
| | - E Jayadevi Variyar
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - Shaik Anwar
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - C Sadasivan
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - R V Omkumar
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
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Dai Q, Yan Y, Ning X, Li G, Yu J, Deng J, Yang L, Li GB. AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo- β-lactamases and indoleamine/tryptophan 2,3-dioxygenases. Acta Pharm Sin B 2021; 11:1931-1946. [PMID: 34386329 PMCID: PMC8343198 DOI: 10.1016/j.apsb.2021.01.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/25/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022] Open
Abstract
We herein describe AncPhore, a versatile tool for drug discovery, which is characterized by pharmacophore feature analysis and anchor pharmacophore (i.e., most important pharmacophore features) steered molecular fitting and virtual screening. Comparative analyses of numerous protein–ligand complexes using AncPhore revealed that anchor pharmacophore features are biologically important, commonly associated with protein conservative characteristics, and have significant contributions to the binding affinity. Performance evaluation of AncPhore showed that it had substantially improved prediction ability on different types of target proteins including metalloenzymes by considering the specific contributions and diversity of anchor pharmacophore features. To demonstrate the practicability of AncPhore, we screened commercially available chemical compounds and discovered a set of structurally diverse inhibitors for clinically relevant metallo-β-lactamases (MBLs); of them, 4 and 6 manifested potent inhibitory activity to VIM-2, NDM-1 and IMP-1 MBLs. Crystallographic analyses of VIM-2:4 complex revealed the precise inhibition mode of 4 with VIM-2, highly consistent with the defined anchor pharmacophore features. Besides, we also identified new hit compounds by using AncPhore for indoleamine/tryptophan 2,3-dioxygenases (IDO/TDO), another class of clinically relevant metalloenzymes. This work reveals anchor pharmacophore as a valuable concept for target-centered drug discovery and illustrates the potential of AncPhore to efficiently identify new inhibitors for different types of protein targets.
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Key Words
- AMPC, asian mouse phenotyping consortium
- AP, anchor pharmacophore
- AR, aromatic ring
- AUC, area under the curve
- Anchor pharmacophore
- BACE1, beta-secretase 1
- BRD4, bromodomain-containing protein 4
- CA, carbonic anhydrase
- CA2, carbonic anhydrase 2
- CDK2, cyclin-dependent kinase 2
- CTS, cathepsins
- CV, covalent bonding
- CatK, cathepsin K
- EF, enrichment factor
- EX, exclusion volume
- GA, genetic algorithm
- HA, hydrogen-bond acceptor
- HD, hydrogen-bond donor
- HIV-P, human immunodeficiency virus protease
- HIV1-P, human immunodeficiency virus type 1 protease
- HY, hydrophobic
- IDO1, indoleamine 2,3-dioxygenase 1
- IMP, imipenemase
- Indoleamine 2,3-dioxygenase
- LE, ligand efficiency
- MAPK14, mitogen-activated protein kinase 14
- MB, metal coordination
- MBL, metallo-β-lactamase
- MIC, minimum inhibitory concentration
- MMP, matrix metalloproteinase
- MMP13, matrix metallopeptidase 13
- Metallo-β-lactamase
- Metalloenzyme
- NDM, new delhi MBL
- NE, negatively charged center
- NP, without anchor pharmacophore features
- PO, positively charged center
- RMSD, root mean square deviation
- ROC curve, receiver operating characteristic curve
- ROCK1, rho-associated protein kinase 1
- RT, reverse transcriptase
- RTK, receptor tyrosine kinase
- SBL, serine beta lactamase
- SSEL, secondary structure element length
- STK, serine threonine kinase
- TDO, tryptophan 2,3-dioxygenase
- TDSS, torsion-driving systematic search
- TNKS2, tankyrase 2
- Tryptophan 2,3-dioxygenase
- VEGFR2, vascular endothelial growth factor receptor 2
- VIM, verona integron-encoded MBL
- Virtual screening
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Yazhini A, Sandhya S, Srinivasan N. Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. Curr Res Struct Biol 2021; 3:133-145. [PMID: 35028595 PMCID: PMC8714771 DOI: 10.1016/j.crstbi.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of homologous and functionally equivalent multiprotein assemblies is intriguing considering sequence divergence of constituent proteins. Here, we studied the implications of protein sequence divergence on the structure, dynamics and function of homologous yeast and human SF3b spliceosomal subcomplexes. Human and yeast SF3b comprise of 7 and 6 proteins respectively, with all yeast proteins homologous to their human counterparts at moderate sequence identity. SF3b6, an additional component in the human SF3b, interacts with the N-terminal extension of SF3b1 while the yeast homologue Hsh155 lacks the equivalent region. Through detailed homology studies, we show that SF3b6 is absent not only in yeast but in multiple lineages of eukaryotes implying that it is critical in specific organisms. We probed for the potential role of SF3b6 in the spliceosome assembled form through structural and flexibility analyses. By analysing normal modes derived from anisotropic network models of SF3b1, we demonstrate that when SF3b1 is bound to SF3b6, similarities in the magnitude of residue motions (0.86) and inter-residue correlated motions (0.94) with Hsh155 are significantly higher than when SF3b1 is considered in isolation (0.21 and 0.89 respectively). We observed that SF3b6 promotes functionally relevant 'open-to-close' transition in SF3b1 by enhancing concerted residue motions. Such motions are found to occur in the Hsh155 without SF3b6. The presence of SF3b6 influences motions of 16 residues that interact with U2 snRNA/branchpoint duplex and supports the participation of its interface residues in long-range communication in the SF3b1. These results advocate that SF3b6 potentially acts as an allosteric regulator of SF3b1 for BPS selection and might play a role in alternative splicing. Furthermore, we observe variability in the relative orientation of SF3b4 and in the local structure of three β-propeller domains of SF3b3 with reference to their yeast counterparts. Such differences influence the inter-protein interactions of SF3b between these two organisms. Together, our findings highlight features of SF3b evolution and suggests that the human SF3b may have evolved sophisticated mechanisms to fine tune its molecular function.
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Key Words
- Allostery
- BPS, branch-point sequence
- Bact, activated B spliceosome assembly
- Cryo-EM structure
- Cryo-EM, cryo-electron microscopy
- DOPE, discrete optimized protein energy
- NMA, normal mode analysis
- PDB, protein data bank
- Protein dynamics
- RMSD, root mean square deviation
- RRM, RNA recognition motif
- SF3b complex
- SF3b1
- SF3b1SF3b6−bound, SF3b1 bound to SF3b6
- SF3b1iso, SF3b1 in isolation
- SIP, square inner product
- Spliceosome
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of alkaloids from Justicia adhatoda as potent SARS CoV-2 main protease inhibitors: An in silico perspective. J Mol Struct 2021; 1229:129489. [PMID: 33100380 PMCID: PMC7571971 DOI: 10.1016/j.molstruc.2020.129489] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/17/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic, caused by SARS CoV-2, is responsible for millions of death worldwide. No approved/proper therapeutics is currently available which can effectively combat this outbreak. Several attempts have been undertaken in the search of effective drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro), key component for the cleavage of the viral polyprotein, is considered to be one of the important drug targets for treating COVID-19. Various phytochemicals, including polyphenols and alkaloids, have been proposed as potent inhibitors of Mpro. The alkaloids from leaf extracts of Justicia adhatoda have also been reported to possess anti-viral activity. But whether these alkaloids exhibit any inhibitory effect on SARS CoV-2 Mpro is far from clear. To explore this in detail, we have adopted computational approaches. Justicia adhatoda alkaloids possessing proper drug-likeness properties and two anti-HIV drugs (lopinavir and darunavir; having binding affinity -7.3 to -7.4 kcal/mol) were docked against SARS CoV-2 Mpro to study their binding properties. Only one alkaloid (anisotine) had interaction with both the catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (-7.9 kcal/mol). Molecular dynamic simulations (100 ns) revealed that Mpro-anisotine complex is more stable, conformationally less fluctuated; slightly less compact and marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of intermolecular H-bonds and MM-GBSA analysis suggested that anisotine is a more potent Mpro inhibitor than the two previously recommended antiviral drugs (lopinavir and darunavir) and may evolve as a promising anti-COVID-19 drug if proven in animal experiments and on patients.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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Benedetti F, Stracke F, Stadlmayr G, Stadlbauer K, Rüker F, Wozniak-Knopp G. Bispecific antibodies with Fab-arms featuring exchanged antigen-binding constant domains. Biochem Biophys Rep 2021; 26:100959. [PMID: 33718630 PMCID: PMC7920882 DOI: 10.1016/j.bbrep.2021.100959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/16/2020] [Accepted: 02/16/2021] [Indexed: 12/27/2022] Open
Abstract
Monoclonal antibodies can acquire the property of engagement of a second antigen via fusion methods or modification of their CDR loops, but also by modification of their constant domains, such as in the mAb2 format where a set of mutated amino acid residues in the CH3 domains enables a high-affinity specific interaction with the second antigen. We tested the possibility of introducing multiple binding sites for the second antigen by replacing the Fab CH1/CL domain pair with a pair of antigen-binding CH3 domains in a model scaffold with trastuzumab variable domains and VEGF-binding CH3 domains. Such bispecific molecules were produced in a “Fab-like” format and in a full-length antibody format. Novel constructs were of expected molecular composition using mass spectrometry. They were expressed at a high level in standard laboratory conditions, purified as monomers with Protein A and gel filtration and were of high thermostability. Their high-affinity binding to both target antigens was retained. Finally, the Her2/VEGF binding domain-exchanged bispecific antibody was able to mediate a potentiated surface Her2-internalization effect on the Her2-overexpressing cell line SK-BR-3 due to improved level of cross-linking with the endogenously secreted cytokine. To conclude, bispecific antibodies with Fabs featuring exchanged antigen-binding CH3 domains offer an alternative solution in positioning and valency of antigen binding sites. Fab constant domains can be efficiently exchanged for antigen-binding CH3 domains. Such mutagenesis results in bispecific antibodies with correct chain pairing. Domain-exchanged bispecific Fab- and IgG-like formats are of favorable biophysical properties. Resulting bispecific antibodies show high-affinity binding to both target antigens.
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Key Words
- Ab, antibody
- BLI, biolayer interferometry
- BSA, bovine serum albumin
- Bispecific antibody
- CDR, complementarity determining region
- DSC, differential scanning calorimetry
- Domain-exchanged antibody
- EC50, half-maximal effective concentration
- FBS, fetal bovine serum
- FITC, fluorescein isothiocyanate
- Fab constant domain exchange
- Fab, fragment antigen binding
- Fc, fragment crystallizable
- Fcab, Fc with antigen binding properties
- HPLC-SEC, high pressure liquid chromatography-size exclusion chromatography
- Her2 internalization
- IgG, immunoglobulin G
- LC-ESI-MS, liquid chromatography-electrospray ionization-mass spectrometry
- PBS, phosphate buffered saline
- PE, phycoerythrin
- PEI, polyethylenimine
- PNGase F, Peptide:N-glycosidase F
- RMSD, root mean square deviation
- TRA, trastuzumab
- Tm, melting temperature
- VEGF, vascular endothelial growth factor
- “Knobs-into-holes” heterodimerization
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Affiliation(s)
- Filippo Benedetti
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Stracke
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Gerhard Stadlmayr
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Katharina Stadlbauer
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Rüker
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Gordana Wozniak-Knopp
- CD Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190, Vienna, Austria
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9
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Gurung AB. In silico structure modelling of SARS-CoV-2 Nsp13 helicase and Nsp14 and repurposing of FDA approved antiviral drugs as dual inhibitors. Gene Rep 2020; 21:100860. [PMID: 32875166 PMCID: PMC7452913 DOI: 10.1016/j.genrep.2020.100860] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022]
Abstract
The high mortality rate from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in humans and the lack of effective therapeutic regime for its treatment necessitates the identification of new antivirals. SARS-CoV-2 relies on non-structural proteins such as Nsp13 helicase and nsp14 which are the key components of the replication-transcription complex (RTC) to complete its infectious life cycle. Therefore, targeting these essential viral proteins with small molecules will most likely to halt the disease pathogenesis. The lack of experimental structures of these proteins deters the process of structure-based identification of their specific inhibitors. In the present study, the in silico models of SARS-CoV-2 nsp13 helicase and nsp14 protein were elucidated using a comparative homology modelling approach. These in silico model structures were validated using various parameters such as Ramachandran plot, Verify 3D score, ERRAT score, knowledge-based energy and Z-score. The in silico models were further used for virtual screening of the Food and Drug Administration (FDA) approved antiviral drugs. Simeprevir (SMV), Paritaprevir (PTV) and Grazoprevir (GZR) were the common leads identified which show higher binding affinity to both nsp13 helicase and nsp14 as compared to the control inhibitors and therefore, they might be potential dual-target inhibitors. The leads also establish a network of hydrogen bonds and hydrophobic interactions with the key residues lining the active site pockets. The present findings suggest that these FDA approved antiviral drugs can be subjected to repurposing against SARS-CoV-2 infection after verifying the in silico results through in vitro and in vivo studies.
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Key Words
- 3CLpro, 3C-like proteinase
- COVID-19
- COVID-19, coronavirus disease 2019
- DOPE, discrete optimized protein energy
- FDA approved antiviral drugs
- FDA, Food and Drug Administration
- GRAVY, grand average of hydropathicity
- GZR, Grazoprevir
- GpppA, Guanosine-P3-adenosine-5′,5′-triphosphate
- Homology modelling
- MERS-CoV, Middle East respiratory syndrome coronavirus
- Molecular docking
- N7-MTase, S-adenosyl methionine (SAM)-dependent (guanine-N7) methyltransferase
- Nsp13 helicase
- Nsp14
- Nsps, non-structural proteins
- PDB, protein data bank
- PLpro, papain-like proteinase
- PTV, Paritaprevir
- RMSD, root mean square deviation
- RTC, replication-transcription complex
- RdRp, RNA-dependent RNA polymerase
- SAH, S-adenosyl homocysteine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SAVES, Structure Analysis and Verification Server
- SF, Sinefungin
- SMV, Simeprevir
- TMHs, transmembrane helices
- ZBD, zinc binding domain
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Affiliation(s)
- Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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10
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Sato Y, Yabuki T, Adachi N, Moriya T, Arakawa T, Kawasaki M, Yamada C, Senda T, Fushinobu S, Wakagi T. Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii. J Struct Biol X 2020; 4:100030. [PMID: 32775998 PMCID: PMC7398979 DOI: 10.1016/j.yjsbx.2020.100030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
Sulfur oxygenase reductase (SOR) was biochemically and structurally characterized. High resolution structures of SOR were determined by crystallography and cryo-EM. Twenty-four identical subunits of SOR form a hollow sphere. Catalytic components exhibited different features in the crystal and cryo-EM structures.
Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of S. tokodaii (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.
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Key Words
- AaSOR, Acidianus ambivalens SOR
- AqSOR, Aquifex aeolicus SOR
- Archaea
- AtSOR, Acidianus tengchongensis SOR
- CTF, contrast transfer function
- Cryogenic electron microscopy
- DTNB, 5,5′-dithiobis(2-nitrobenzoic acid)
- FSC, Fourier shell correlation
- HnSOR, Halothiobacillus neapolitanus SOR
- Nonheme mononuclear iron center
- PAGE, polyacrylamide gel electrophoresis
- RMSD, root mean square deviation
- SD, standard deviation
- SDS, sodium dodecyl sulfate
- SOR, sulfur oxygenase reductase
- SbSOR, Sulfobacillus thermosulfidooxidans SOR
- StSOR, Sulfurisphaera tokodaii SOR
- Sulfur metabolism
- TpSOR, Thioalkalivibrio paradoxus SOR
- X-ray crystallography
- cryo-EM, cryogenic electron microscopy
- pCMB, p-chloromercuribenzoate
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Affiliation(s)
- Yuta Sato
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Yabuki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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11
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Yu D, Zou J, Chen Q, Zhu T, Sui R, Yang J. Structural modeling, mutation analysis, and in vitro expression of usherin, a major protein in inherited retinal degeneration and hearing loss. Comput Struct Biotechnol J 2020; 18:1363-1382. [PMID: 32637036 PMCID: PMC7317166 DOI: 10.1016/j.csbj.2020.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/15/2022] Open
Abstract
Usherin is the most common causative protein associated with autosomal recessive retinitis pigmentosa (RP) and Usher syndrome (USH), which are characterized by retinal degeneration alone and in combination with hearing loss, respectively. Usherin is essential for photoreceptor survival and hair cell bundle integrity. However, the molecular mechanism underlying usherin function in normal and disease conditions is unclear. In this study, we investigated structural models of usherin domains and localization of usherin pathogenic small in-frame mutations, mainly homozygous missense mutations. We found that usherin fibronectin III (FN3) domains and most laminin-related domains have a β-sandwich structure. Some FN3 domains are predicted to interact with each other and with laminin-related domains. The usherin protein may bend at some FN3 linker regions. RP- and USH-associated small in-frame mutations are differentially located in usherin domains. Most of them are located at the periphery of β-sandwiches, with some at the interface between interacting domains. The usherin laminin epidermal growth factor repeats adopt a rod-shaped structure, which is maintained by disulfide bonds. Most missense mutations and deletion of exon 13 in this region disrupt the disulfide bonds and may affect local protein folding. Despite low expression of the recombinant entire protein and protein fragments in mammalian cell culture, usherin FN3 fragments are more robustly expressed and secreted than its laminin-related fragments. Our findings provide new insights into the usherin structure and the disease mechanisms caused by pathogenic small in-frame mutations, which will help inform future experimental research on diagnosis, disease mechanisms, and therapeutic approaches.
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Key Words
- Cell adhesion
- DCC, deleted in colorectal cancer
- FN3, fibronectin III
- GMQE, global quality estimation score
- HGMD, Human Gene Mutation Database
- Hair cell
- I-TASSER, Iterative Threading ASSEmbly Refinement
- LE, laminin EGF
- LG, laminin globular
- LGL, laminin globular-like
- LN, laminin N-terminal
- Membrane protein
- NCBI, National Center for Biotechnology Information
- Photoreceptor
- Protein folding
- QMEAN, qualitative model energy analysis score
- QSQE, Quaternary Structure Quality Estimation
- RMSD, root mean square deviation
- RP, retinitis pigmentosa
- Recombinant protein expression
- Retinitis pigmentosa
- SMTL, SWISS-MODEL template library
- Structural model
- TM-score, template modeling score
- USH, Usher syndrome
- Usher syndrome
- hFc, human Fc fragment
- mFc, mouse Fc fragment
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Affiliation(s)
- Dongmei Yu
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Qian Chen
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
- Division of Otolaryngology, Department of Surgery, University of Utah, Salt Lake City, UT, United States
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12
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Fernández-de Gortari E, Aguayo-Ortiz R, Autry JM, Michel Espinoza-Fonseca L. A hallmark of phospholamban functional divergence is located in the N-terminal phosphorylation domain. Comput Struct Biotechnol J 2020; 18:705-713. [PMID: 32257054 PMCID: PMC7114604 DOI: 10.1016/j.csbj.2020.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/23/2020] [Accepted: 02/23/2020] [Indexed: 01/12/2023] Open
Abstract
Sarcoplasmic reticulum Ca2+ pump (SERCA) is a critical component of the Ca2+ transport machinery in myocytes. There is clear evidence for regulation of SERCA activity by PLB, whose activity is modulated by phosphorylation of its N-terminal domain (residues 1–25), but there is less clear evidence for the role of this domain in PLB’s functional divergence. It is widely accepted that only sarcolipin (SLN), a protein that shares substantial homology with PLB, uncouples SERCA Ca2+ transport from ATP hydrolysis by inducing a structural change of its energy-transduction domain; yet, experimental evidence shows that the transmembrane domain of PLB (residues 26–52, PLB26–52) partially uncouples SERCA in vitro. These apparently conflicting mechanisms suggest that PLB’s uncoupling activity is encoded in its transmembrane domain, and that it is controlled by the N-terminal phosphorylation domain. To test this hypothesis, we performed molecular dynamics simulations (MDS) of the binary complex between PLB26–52 and SERCA. Comparison between PLB26–52 and wild-type PLB (PLBWT) showed no significant changes in the stability and orientation of the transmembrane helix, indicating that PLB26–52 forms a native-like complex with SERCA. MDS showed that PLB26–52 produces key intermolecular contacts and structural changes required for inhibition, in agreement with studies showing that PLB26–52 inhibits SERCA. However, deletion of the N-terminal phosphorylation domain facilitates an order-to-disorder shift in the energy-transduction domain associated with uncoupling of SERCA, albeit weaker than that induced by SLN. This mechanistic evidence reveals that the N-terminal phosphorylation domain of PLB is a primary contributor to the functional divergence among homologous SERCA regulators.
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Affiliation(s)
- Eli Fernández-de Gortari
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rodrigo Aguayo-Ortiz
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph M Autry
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Biophysical Technology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Gogoi P, Kanaujia SP. Role of Structural Features in Oligomerization, Active-Site Integrity and Ligand Binding of Ribose-1,5-Bisphosphate Isomerase. Comput Struct Biotechnol J 2019; 17:333-344. [PMID: 30923607 PMCID: PMC6423476 DOI: 10.1016/j.csbj.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 11/18/2022] Open
Abstract
Pentose bisphosphate pathway, exclusively found in archaea, is similar to the pentose phosphate pathway present in bacteria and eukarya. In pentose bisphosphate pathway, the conversion of ribose moieties of nucleosides into 3-phosphoglycerate (3-PGA) involves multiple steps; one of them being the conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) catalyzed by an enzyme ribose-1,5-bisphosphate isomerase (R15Pi). The availability of the three-dimensional structure of R15Pi had facilitated the understanding of various structural and functional aspects of the enzyme. Nevertheless, the structure of R15Pi also left several significant questions unanswered that would aid in understanding the structure-function relationship of the enzyme. Thus, we have taken up a computational approach to further understand the role of various structural features of the enzyme R15Pi. Results obtained from molecular dynamics (MD) simulations aided in understanding the obligation of the enzyme R15Pi to oligomerize and also in deciphering the role of catalytic residue(s) in structural stability. Identification of invariant water molecules of the enzyme R15Pi helped in discerning their significance at the active-site pocket and structurally important regions. Further, molecular docking studies allowed the identification of the amino acid residues essential for holding the substrate (R15P) or product (RuBP) in the vicinity of the active site of the enzyme R15Pi. Interestingly, results of the molecular docking studies assisted in the identification of an “alternate binding site” for the substrate, R15P. Finally, based on these results, we propose a mechanism of “substrate sliding” for the enzyme R15Pi. Hexameric state is obligatory for the functionality of R15Pi. Cysteine is more important catalytic residue than aspartate. Invariant water molecules are conserved at the active site and structurally important areas. The substrate does not directly bind to the active site. The substrate slides from the “initial binding site” to the active site.
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Key Words
- 3-PGA, 3-phosphoglycerate
- ADP-R1P, ADP-dependentribose-1-phosphate
- ASU, asymmetric unit
- EFBE, estimated free energy of binding
- Invariant water molecule
- LGA, Lamarckian genetic algorithm
- MD, molecular dynamics
- Molecular docking
- Molecular dynamics simulation
- NMP, nucleoside 5′-monophosphate
- Nucleoside 5′-monophosphate degradation pathway
- R15P, ribose-1,5-bisphosphate
- R15Pi, ribose-1,5-bisphosphate isomerase
- R1P, ribose-1-phosphate
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- Ribose-1,5-bisphosphate
- Ribulose-1,5-bisphosphate
- RuBP, ribulose-1,5-bisphosphate
- RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase
- SASA, solvent accessible surface area
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Ozsvar J, Tarakanova A, Wang R, Buehler MJ, Weiss AS. Allysine modifications perturb tropoelastin structure and mobility on a local and global scale. Matrix Biol Plus 2019; 2:100002. [PMID: 33543005 PMCID: PMC7852328 DOI: 10.1016/j.mbplus.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/10/2019] [Accepted: 03/10/2019] [Indexed: 11/20/2022] Open
Abstract
Elastin provides elastic tissues with resilience through stretch and recoil cycles, and is primarily made of its extensively cross-linked monomer, tropoelastin. Here, we leverage the recently published full atomistic model of tropoelastin to assess how allysine modifications, which are essential to cross-linking, contribute to the dynamics and structural changes that occur in tropoelastin in the context of elastin assembly. We used replica exchange molecular dynamics to generate structural ensembles of allysine containing tropoelastin. We conducted principal component analysis on these ensembles and found that the molecule departs from the canonical structural ensemble. Furthermore, we showed that, while the canonical scissors-twist movement was retained, new movements emerged that deviated from those of the wild type protein, providing evidence for the involvement of a variety of molecular motions in elastin assembly. Additionally, we highlighted secondary structural changes and linked these perturbations to the longevity of specific salt bridges. We propose a model where allysines in tropoelastin contribute to hierarchical elastin assembly through global and local perturbations to molecular structure and dynamics. converting lysine to allysine by lysyl oxidases is needed to generate crosslinks between tropoelastin molecules in order to make elastin structural changes in the intact tropoelastin molecule ensue where modified tropoelastin molecules structurally depart from the canonical ensemble new molecular motions deviate from those of unmodified tropoelastin persistence times of specific salt bridges contribute to these perturbations allysines in tropoelastin contribute to hierarchical elastin assembly through global and local perturbations to molecular structure and dynamics
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Key Words
- 5ALK, tropoelastin containing 5 allysine residues
- ALK353, tropoelastin containing allysine at residue 353
- ALK353, tropoelastin containing allysine at residue 507
- ALL, allysine aldol
- ANM, anisotropic network model
- Assembly
- ECM, extracellular matrix
- Elastin
- LNL, lysinonorleucine
- MD, molecular dynamics
- Molecular dynamics
- NMA, normal mode analysis
- PCA, principal component analysis
- REMD, replica exchange molecular dynamics
- RMSD, root mean square deviation
- Replica exchange molecular dynamics
- SASA, solvent accessible surface area
- WT, wild type tropoelastin
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Affiliation(s)
- Jazmin Ozsvar
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia.,Cell Therapy Manufacturing Cooperative Research Centre, Adelaide, 5000, SA, Australia
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richard Wang
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony S Weiss
- Charles Perkins Centre, the University of Sydney, 2006 Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, 2006 Sydney, NSW, Australia.,Cell Therapy Manufacturing Cooperative Research Centre, Adelaide, 5000, SA, Australia.,Bosch Institute, The University of Sydney, 2006 Sydney, NSW, Australia.,Sydney Nano Institute, The University of Sydney, 2006 Sydney, NSW, Australia
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15
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Cruz JN, Costa JFS, Khayat AS, Kuca K, Barros CAL, Neto AMJC. Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13. J Biomol Struct Dyn 2018; 37:1616-1627. [PMID: 29633908 DOI: 10.1080/07391102.2018.1462734] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.
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Key Words
- CNPq, National Council for Scientific and Technological Development
- CoA, coenzyme A
- FAS, fatty acid synthase
- GAFF, general amber force field
- GB, generalized born
- HB, hydrogen bonds
- INH, isoniazid
- KatG, catalase-peroxidase
- MD, molecular dynamics
- MDR, multi-drug resistant
- MM/GBSA, molecular mechanics/generalized-born surface area
- NAD, nicotinamide adenine dinucleotide
- NS, nanoseconds
- PCA, acyl carrier protein
- Pks13
- Pks13, polyketide synthase 13
- RESP, restrained electrostatic potential
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- TB, tuberculosis
- TE, C-terminal thioesterase
- XDR, extensively drug resistant
- benzofuran
- free energy
- inhibitors
- molecular dynamics
- Δ internal energy
- Δ, Van Der Waals contributions
- Δ, electrostatic contribution
- Δ, electrostatic contributions
- Δ, energy of desolvation
- Δ, energy of the molecular mechanics
- Δ, non-polar contributions
- Δ, polar contributions
- Δ, polar solvation contribution
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Affiliation(s)
- Jorddy N Cruz
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - José F S Costa
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - André S Khayat
- b Oncology Research Center , Federal University of Pará , CP 479, 6675-105 Belém , PA , Brazil
| | - Kamil Kuca
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic
| | - Carlos A L Barros
- d Department of Pharmacy , Federal University of Pará , CP 479, 66050-160 Belém , PA , Brazil
| | - A M J C Neto
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
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Kumar R, Jade D, Gupta D. A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening, molecular docking and molecular dynamics. J Biomol Struct Dyn 2018; 37:931-943. [PMID: 29468945 DOI: 10.1080/07391102.2018.1444509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study, we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology-based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer. The MD simulations of the shortlisted compounds in complex with 5-HydroxyTriptamine 2A confirmed the stability of the complexes and revealed novel interaction insights. The receptor residues S239, N343, S242, S159, Y370 and D155 predominantly participate in hydrogen bonding. π-π stacking is observed in F339, F340, F234, W151 and W336, whereas hydrophobic interactions are observed amongst V156, F339, F234, V362, V366, F340, V235, I152 and W151. The known and potential antagonists shortlisted by us have similar overlapping molecular interaction patterns. The 287 potential 5-HydroxyTriptamine 2A antagonists may be experimentally verified.
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Key Words
- , tanimoto coefficient
- 2D similarity
- 2D, two-dimensional space
- 2D/3D screening
- 3D similarity
- 3D, three-dimensional space
- 5HT
- 5HT, 5-HydroxyTryptamine
- ADHD, attention deficit hyperactivity disorders
- BLAST, basic local alignment search tool
- CNS, central nervous system
- Cl ions, chloride ions
- DOPE, discrete optimized protein energy
- G-protein coupled receptor
- GPCRs, G protein-coupled receptors
- HB, hydrogen bond
- HBA, hydrogen bond acceptors
- HBD, hydrogen bond donors
- JC virus, John Cunningham virus
- Ki, equilibrium dissociation constant for the ligand
- LBVS, ligand-based virtual screening
- MD, molecular dynamic
- MSD, mean square displacement
- MW, molecular weight
- NHB, number of hydrogen bonds
- OCD, obsessive compulsive disorder
- P5/P95, percentile calculation
- PAINS, Pan assay interference compounds
- PDB, protein data bank
- PLIP, protein–ligand interaction profiler
- PME, Particle Mesh Ewald
- PNS, peripheral nervous system
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- Rg, radius of gyration
- SASA, solvent accessible surface area
- SCA, stochastic clustering algorithm
- SD, steepest descent
- SDF, structure data file
- SPC, single point charge
- SPD, simple point charge
- SSE, secondary structure elements
- Sn-1/sn-2, Stereospecific number
- TM, Transmembrane
- TPSA, topological polar surface area
- drug discovery
- fs, femtosecond
- kJ/mol, kilo Joule per mol
- kcal/mol, kilocalorie per mole sn-1
- ligand-based virtual screening
- nm, nanomolar
- ns, nanosecond
- Å Ångström
- β2-AR, β2 adrenergic receptor
- μM, micromolar
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Affiliation(s)
- Rakesh Kumar
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
| | - Dhananjay Jade
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
| | - Dinesh Gupta
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
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Meshach Paul D, Chadah T, Senthilkumar B, Sethumadhavan R, Rajasekaran R. Structural distortions due to missense mutations in human formylglycine-generating enzyme leading to multiple sulfatase deficiency. J Biomol Struct Dyn 2017; 36:3575-3585. [PMID: 29048999 DOI: 10.1080/07391102.2017.1394220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The major candidate for multiple sulfatase deficiency is a defective formylglycine-generating enzyme (FGE). Though adequately produced, mutations in FGE stall the activation of sulfatases and prevent their activity. Missense mutations, viz. E130D, S155P, A177P, W179S, C218Y, R224W, N259I, P266L, A279V, C336R, R345C, A348P, R349Q and R349W associated with multiple sulfatase deficiency are yet to be computationally studied. Aforementioned mutants were initially screened through ws-SNPs&GO3D program. Mutant R345C acquired the highest score, and hence was studied in detail. Discrete molecular dynamics explored structural distortions due to amino acid substitution. Therein, comparative analyses of wild type and mutant were carried out. Changes in structural contours were observed between wild type and mutant. Mutant had low conformational fluctuation, high atomic mobility and more compactness than wild type. Moreover, free energy landscape showed mutant to vary in terms of its conformational space as compared to wild type. Subsequently, wild type and mutant were subjected to single-model analyses. Mutant had lesser intra molecular interactions than wild type suggesting variations pertaining to its secondary structure. Furthermore, simulated thermal denaturation showed dissimilar pattern of hydrogen bond dilution. Effects of these variations were observed as changes in elements of secondary structure. Docking studies of mutant revealed less favourable binding energy towards its substrate as compared to wild type. Therefore, theoretical explanations for structural distortions of mutant R345C leading to multiple sulfatase deficiency were revealed. The protocol of the study could be useful to examine the effectiveness of pharmacological chaperones prior to experimental studies.
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Key Words
- , sulfatase-modifying factor
- ARSB, aryl sulfatase B
- AUC, area under the curve
- DMD, discrete molecular dynamics
- FEL, free energy landscape
- FGE, formylglycine-generating enzyme
- FGly, formylglycine
- LSD, lysosomal storage disorder
- MCC, Mathew’s correlation coeffecient
- MD, molecular dynamics
- MSD, multiple sulfatase defeciency
- PCA, principal component analysis
- PDB, Protein Data Bank
- PIC, protein interaction calculator
- RCSB, Research Collaboratory for Structural Bioinformatics
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- RoG, radius of gyration
- SVM-3D, support vector machine-3D
- discrete molecular dynamics
- free energy landscape
- genetic disorder
- lysosomal storage disorder
- misfolding
- multiple sulfatase
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Affiliation(s)
- D Meshach Paul
- a Department of Biotechnology, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - Tania Chadah
- a Department of Biotechnology, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - B Senthilkumar
- a Department of Biotechnology, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - Rao Sethumadhavan
- a Department of Biotechnology, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
| | - R Rajasekaran
- a Department of Biotechnology, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamil Nadu , India
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Abstract
Knowledge of the 3-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 Å on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures.
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Affiliation(s)
- Alexander Bujotzek
- a Roche Pharmaceutical Research and Early Development; Large Molecule Research; Roche Innovation Center Penzberg ; Penzberg , Germany
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Tomonaga Y, Kaneko R, Goto M, Ohshima T, Yoshimune K. Structural insight into activation of homoserine dehydrogenase from the archaeon Sulfolobus tokodaii via reduction. Biochem Biophys Rep 2015; 3:14-17. [PMID: 29124164 PMCID: PMC5668673 DOI: 10.1016/j.bbrep.2015.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/13/2015] [Accepted: 07/13/2015] [Indexed: 10/27/2022] Open
Abstract
Homoserine dehydrogenase (HSD; 305 amino acid residues) catalyzes an NAD(P)-dependent reversible reaction between l-homoserine and aspartate 4-semialdehyde and is involved in the aspartate pathway. HSD from the hyperthermophilic archaeon Sulfolobus tokodaii was markedly activated (2.5-fold) by the addition of 0.8 mM dithiothreitol. The crystal structure of the homodimer indicated that the activation was caused by cleavage of the disulfide bond formed between two cysteine residues (C303) in the C-terminal regions of the two subunits.
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Key Words
- Activation
- Bis-tris, 2,2-bis(hydroxymethyl)-2,2′,2″-nitrilotriethanol
- Crystal structure
- DMSO, dimethyl sulfoxide
- DTT, dithiothreitol
- Disulfide bond
- HEPES, [4-(2-hydroxyethyl)-1-piperazinyl] ethanesulfonic acid
- HSD, homoserine dehydrogenase
- Homoserine dehydrogenase
- Hyperthermophilic archaea
- IPTG, isopropyl 1-thio-β-d-galactoside
- KPB, potassium phosphate buffer
- LB medium, Luria-Bertani medium
- ORF, open reading frame
- PDB, Protein Data Bank
- PEG, poly(ethylene glycol)
- RMSD, root mean square deviation
- SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- Tricine, N-[tris(hydroxymethyl)methyl]glycine
- Tris, tris(hydroxymethyl)aminomethane
- mPMS, 1-methoxy-5-methyl-phenazinium methyl sulfate
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Affiliation(s)
- Yoshihisa Tomonaga
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba 275-8575, Japan
| | - Ryosuke Kaneko
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Kazuaki Yoshimune
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba 275-8575, Japan
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Ambrus A, Mizsei R, Adam-Vizi V. Structural alterations by five disease-causing mutations in the low-pH conformation of human dihydrolipoamide dehydrogenase (hLADH) analyzed by molecular dynamics - Implications in functional loss and modulation of reactive oxygen species generation by pathogenic hLADH forms. Biochem Biophys Rep 2015; 2:50-56. [PMID: 29594200 PMCID: PMC5871931 DOI: 10.1016/j.bbrep.2015.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/25/2015] [Accepted: 04/27/2015] [Indexed: 01/12/2023] Open
Abstract
Human dihydrolipoamide dehydrogenase (hLADH) is a flavoenzyme component (E3) of the human alpha-ketoglutarate dehydrogenase complex (α-KGDHc) and few other dehydrogenase complexes. Pathogenic mutations of hLADH cause severe metabolic diseases (atypical forms of E3 deficiency) that often escalate to cardiological or neurological presentations and even premature death; the pathologies are generally accompanied by lactic acidosis. hLADH presents a distinct conformation under acidosis (pH 5.5–6.8) with lower physiological activity and the capacity of generating reactive oxygen species (ROS). It has been shown by our laboratory that selected pathogenic mutations, besides lowering the physiological activity of hLADH, significantly stimulate ROS generation by hLADH, especially at lower pH, which might play a role in the pathogenesis of E3-deficiency in respective cases. Previously, we generated by molecular dynamics (MD) simulation the low-pH hLADH structure and analyzed the structural changes induced in this structure by eight of the pathogenic mutations of hLADH. In the absence of high resolution mutant structures these pieces of information are crucial for the mechanistic investigation of the molecular pathogeneses of the hLADH protein. In the present work we analyzed by molecular dynamics simulation the structural changes induced in the low-pH conformation of hLADH by five pathogenic mutations of hLADH; the structures of these disease-causing mutants of hLADH have never been examined before. 5 disease-causing mutants of hLADH were subjected to MD to reveal structural changes. MD simulations were carried out both in vacuum and in water supplemented with ions. Functional regions significantly affected by mutation were identified. Implicated residues are to be targeted in mechanistic studies of hLADH dysfunction.
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Key Words
- FAD, flavin adenine dinucleotide
- LADH, (dihydro)lipoamide dehydrogenase
- Lipoamide dehydrogenase
- MD, molecular dynamics
- Molecular dynamics
- Mutation
- NAD+/NADH, nicotinamide adenine dinucleotide (oxidized/reduced)
- PDHc, pyruvate dehydrogenase complex
- RMSD, root mean square deviation
- ROS, reactive oxygen species
- Reactive oxygen species
- S.E.M., standard error of the mean
- WT, wild-type
- α-KGDHc, alpha-ketoglutarate dehydrogenase complex
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
| | - Reka Mizsei
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest 1094, Hungary
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Rasal KD, Shah TM, Vaidya M, Jakhesara SJ, Joshi CG. Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-β receptor type 3 gene in chicken. Meta Gene 2015; 4:107-17. [PMID: 25941634 PMCID: PMC4412971 DOI: 10.1016/j.mgene.2015.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022] Open
Abstract
The recent advances in high throughput sequencing technology accelerate possible ways for the study of genome wide variation in several organisms and associated consequences. In the present study, mutations in TGFBR3 showing significant association with FCR trait in chicken during exome sequencing were further analyzed. Out of four SNPs, one nsSNP p.Val451Leu was found in the coding region of TGFBR3. In silico tools such as SnpSift and PANTHER predicted it as deleterious (0.04) and to be tolerated, respectively, while I-Mutant revealed that protein stability decreased. The TGFBR3 I-TASSER model has a C-score of 0.85, which was validated using PROCHECK. Based on MD simulation, mutant protein structure deviated from native with RMSD 0.08 Å due to change in the H-bonding distances of mutant residue. The docking of TGFBR3 with interacting TGFBR2 inferred that mutant required more global energy. Therefore, the present study will provide useful information about functional SNPs that have an impact on FCR traits. Investigated functional nsSNP p.Val451Leu (rs312979494) in feed conversion ratio (FCR) associated TGFBR3 of chicken Computational tools (SIFT and I-Mutant 2.0) predicted that this nsSNP was deleterious. Mutant structure of TGFBR3 showed high energies and RMS deviations compared to native using MD simulation. Molecular docking of TGFBR3 with interacting protein TGFBR2 showed an increase in global energy of mutant compared to native. We have predicted that functional SNP has an impact on TGFBR3 of chicken and thus can be treated as candidate SNP in screening.
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Key Words
- AASs, amino acid substitutions
- Chicken
- FCR, feed conversion ratio
- Feed conversion ratio (FCR)
- I-TASSER, iterative threading assembly refinement
- MD, molecular dynamics
- Modeling
- Non-synonymous SNP
- PANTHER, protein analysis through evolutionary relationships
- RMSD, root mean square deviation
- RMSF, root mean square fluctuation
- SIFT, sorting intolerant from tolerant
- SNP, single nucleotide polymorphism
- TGFB, transforming growth factor beta
- TGFBR3
- UTR, un-translated region
- nsSNPs, non-synonymous single nucleotide polymorphisms
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Affiliation(s)
- Kiran D Rasal
- Department of Fish Genetics Biotechnology, Central Institute of Freshwater Aquaculture, ICAR, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Megha Vaidya
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
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Lian K, Leiros HKS, Moe E. MutT from the fish pathogen Aliivibrio salmonicida is a cold-active nucleotide-pool sanitization enzyme with unexpectedly high thermostability. FEBS Open Bio 2015; 5:107-16. [PMID: 25737836 PMCID: PMC4338371 DOI: 10.1016/j.fob.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/27/2015] [Indexed: 02/08/2023] Open
Abstract
Upon infection by pathogenic bacteria, production of reactive oxygen species (ROS) is part of the host organism's first line of defence. ROS damage a number of macromolecules, and in order to withstand such a harsh environment, the bacteria need to have well-functioning ROS scavenging and repair systems. Herein, MutT is an important nucleotide-pool sanitization enzyme, which degrades 8-oxo-dGTP and thus prevents it from being incorporated into DNA. In this context, we have performed a comparative biochemical and structural analysis of MutT from the fish pathogen Aliivibrio salmonicida (AsMutT) and the human pathogen Vibrio cholerae (VcMutT), in order to analyse their function as nucleotide sanitization enzymes and also determine possible cold-adapted properties of AsMutT. The biochemical characterisation revealed that both enzymes possess activity towards the 8-oxo-dGTP substrate, and that AsMutT has a higher catalytic efficiency than VcMutT at all temperatures studied. Calculations based on the biochemical data also revealed a lower activation energy (E a) for AsMutT compared to VcMutT, and differential scanning calorimetry experiments showed that AsMutT displayed an unexpected higher melting temperature (T m) value than VcMutT. A comparative analysis of the crystal structure of VcMutT, determined to 2.42 Å resolution, and homology models of AsMutT indicate that three unique Gly residues in loops of VcMutT, and additional long range ion-pairs in AsMutT could explain the difference in temperature stability of the two enzymes. We conclude that AsMutT is a stable, cold-active enzyme with high catalytic efficiency and reduced E a, compared to the mesophilic VcMutT.
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Affiliation(s)
- Kjersti Lian
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, The Arctic University of Norway, 9037 Tromsø, Norway ; Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República - EAN, 2780-157 Oeiras, Portugal
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23
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Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H. Contribution of histone N-terminal tails to the structure and stability of nucleosomes. FEBS Open Bio 2013; 3:363-9. [PMID: 24251097 PMCID: PMC3821030 DOI: 10.1016/j.fob.2013.08.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/17/2022] Open
Abstract
Histones are the protein components of the nucleosome, which forms the basic architecture of eukaryotic chromatin. Histones H2A, H2B, H3, and H4 are composed of two common regions, the "histone fold" and the "histone tail". Many efforts have been focused on the mechanisms by which the post-translational modifications of histone tails regulate the higher-order chromatin architecture. On the other hand, previous biochemical studies have suggested that histone tails also affect the structure and stability of the nucleosome core particle itself. However, the precise contributions of each histone tail are unclear. In the present study, we determined the crystal structures of four mutant nucleosomes, in which one of the four histones, H2A, H2B, H3, or H4, lacked the N-terminal tail. We found that the deletion of the H2B or H3 N-terminal tail affected histone-DNA interactions and substantially decreased nucleosome stability. These findings provide important information for understanding the complex roles of histone tails in regulating chromatin structure.
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Affiliation(s)
- Wakana Iwasaki
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan ; RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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