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Kumar S, Balaya RDA, Kanekar S, Raju R, Prasad TSK, Kandasamy RK. Computational tools for exploring peptide-membrane interactions in gram-positive bacteria. Comput Struct Biotechnol J 2023; 21:1995-2008. [PMID: 36950221 PMCID: PMC10025024 DOI: 10.1016/j.csbj.2023.02.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 12/21/2022] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The vital cellular functions in Gram-positive bacteria are controlled by signaling molecules known as quorum sensing peptides (QSPs), considered promising therapeutic interventions for bacterial infections. In the bacterial system QSPs bind to membrane-coupled receptors, which then auto-phosphorylate and activate intracellular response regulators. These response regulators induce target gene expression in bacteria. One of the most reliable trends in drug discovery research for virulence-associated molecular targets is the use of peptide drugs or new functionalities. In this perspective, computational methods act as auxiliary aids for biologists, where methodologies based on machine learning and in silico analysis are developed as suitable tools for target peptide identification. Therefore, the development of quick and reliable computational resources to identify or predict these QSPs along with their receptors and inhibitors is receiving considerable attention. The databases such as Quorumpeps and Quorum Sensing of Human Gut Microbes (QSHGM) provide a detailed overview of the structures and functions of QSPs. The tools and algorithms such as QSPpred, QSPred-FL, iQSP, EnsembleQS and PEPred-Suite have been used for the generic prediction of QSPs and feature representation. The availability of compiled key resources for utilizing peptide features based on amino acid composition, positional preferences, and motifs as well as structural and physicochemical properties, including biofilm inhibitory peptides, can aid in elucidating the QSP and membrane receptor interactions in infectious Gram-positive pathogens. Herein, we present a comprehensive survey of diverse computational approaches that are suitable for detecting QSPs and QS interference molecules. This review highlights the utility of these methods for developing potential biomarkers against infectious Gram-positive pathogens.
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Key Words
- 3-HBA, 3–Hydroxybenzoic Acid
- AAC, Amino Acid Composition
- ABC, ATP-binding cassette
- ACD, Available Chemicals Database
- AIP, Autoinducing Peptide
- AMP, Anti-Microbial Peptide
- ATP, Adenosine Triphosphate
- Agr, Accessory gene regulator
- BFE, Binding Free Energy
- BIP Inhibitors
- BIP, Biofilm Inhibitory Peptides
- BLAST, Basic Local Alignment Search Tool
- BNB, Bernoulli Naïve-Bayes
- CADD, Computer-Aided Drug Design
- CSP, Competence Stimulating Peptide
- CTD, Composition-Transition-Distribution
- D, Aspartate
- DCH, 3,3′-(3,4-dichlorobenzylidene)-bis-(4-hydroxycoumarin)
- DT, Decision Tree
- FDA, Food and Drug Administration
- GBM, Gradient Boosting Machine
- GDC, g-gap Dipeptide
- GNB, Gaussian NB
- Gram-positive bacteria
- H, Histidine
- H-Kinase, Histidine Kinase
- H-phosphotransferase, Histidine Phosphotransferase
- HAM, Hamamelitannin
- HGM, Human Gut Microbiota
- HNP, Human Neutrophil Peptide
- IT, Information Theory Features
- In silico approaches
- KNN, K-Nearest Neighbors
- MCC, Mathew Co-relation Coefficient
- MD, Molecular Dynamics
- MDR, Multiple Drug Resistance
- ML, Machine Learning
- MRSA, Methicillin Resistant S. aureus
- MSL, Multiple Sequence Alignment
- OMR, Omargliptin
- OVP, Overlapping Property Features
- PCP, Physicochemical Properties
- PDB, Protein Data Bank
- PPIs, Protein-Protein Interactions
- PSM, Phenol-Soluble Modulin
- PTM, Post Translational Modification
- QS, Quorum Sensing
- QSCN, QS communication network
- QSHGM, Quorum Sensing of Human Gut Microbes
- QSI, QS Inhibitors
- QSIM, QS Interference Molecules
- QSP inhibitors
- QSP predictors
- QSP, QS Peptides
- QSPR, Quantitative Structure Property Relationship
- Quorum sensing peptides
- RAP, RNAIII-activating protein
- RF, Random Forest
- RIP, RNAIII-inhibiting peptide
- ROC, Receiver Operating Characteristic
- SAR, Structure-Activity Relationship
- SFS, Sequential Forward Search
- SIT, Sitagliptin
- SVM, Support Vector Machine
- TCS, Two-Component Sensory
- TRAP, Target of RAP
- TRG, Trelagliptin
- WHO, World Health Organization
- mRMR, minimum Redundancy and Maximum Relevance
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Affiliation(s)
- Shreya Kumar
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore 575018, India
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | | | - Saptami Kanekar
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore 575018, India
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | | | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Gantla MR, Tsigelny IF, Kouznetsova VL. Repurposing of drugs for combined treatment of COVID-19 cytokine storm using machine learning. Med Drug Discov 2023; 17:100148. [PMID: 36466363 PMCID: PMC9706997 DOI: 10.1016/j.medidd.2022.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) induced cytokine storm is the major cause of COVID-19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. We targeted five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor‑Kappa B (NF‑κB), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3), which are involved in the SARS‑CoV‑2 induced cytokine storm pathway. We developed machine-learning (ML) models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find novel therapeutics for COVID‑19. We identified twenty drugs that are active for four proteins with predicted scores greater than 0.8 and eight drugs active for all five proteins with predicted scores over 0.85. Mitomycin C is the most active drug across all five proteins with an average prediction score of 0.886. For further validation of these results, we used the PyRx software to conduct protein-ligand docking experiments and calculated the binding affinity. The docking results support findings by the ML model. This research study predicted that several drugs can target multiple proteins simultaneously in cytokine storm-related pathway. These may be useful drugs to treat patients because these therapies can fight cytokine storm caused by the virus at multiple points of inhibition, leading to synergistically effective treatments.
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Key Words
- 1D 2D 3D, one- two- three-dimensional
- ADAM17, A disintegrin and metalloprotease 17
- ARDS, acute respiratory distress syndrome
- AT1R, Angiotensin II receptor type 1
- AUROC, Area under receiver operator characteristic curve
- COVID-19
- COVID-19, coronavirus disease 2019
- CRS, cytokine release syndrome
- CXCL10, CXC-chemokine ligand 10
- Docking
- FDA, Food and Drug Administration
- G-CSF, granulocyte colony stimulating factor
- IC50, half maximal inhibitory concentration
- ICU, intensive care unit
- IL, interleukin
- JAK1, Janus kinase 1
- MCP1, monocyte chemoattractant protein-1
- MIP1α, macrophage inflammatory protein 1
- ML, machine learning
- Machine learning
- Multi-targeted drug discovery
- NF-κB, Nuclear Factor-Kappa B
- PDB, Protein Data Bank
- PaDEL, Pharmaeutical data exploration laboratory
- ROC, receiver operator characteristic curve
- SARS-CoV-2
- SMILES, Simplified Molecular-Input Line-Entry System
- STAT3, signal transducer and activator of transcription 3
- Screening of FDA-approved drugs
- TNFα, tumor necrosis factor α
- WEKA, Waikato Environment for Knowledge Analysis
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Affiliation(s)
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, Calif, USA
- BiAna, La Jolla, Calif, USA
- Dept. of Neurosciences, UC San Diego, Calif, USA
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Sharifi F, Sharifi I, Babaei Z, Alahdin S, Afgar A. Bioinformatics evaluation of anticancer properties of GP63 protein-derived peptides on MMP2 protein of melanoma cancer. J Pathol Inform 2023; 14:100190. [PMID: 36700237 PMCID: PMC9867975 DOI: 10.1016/j.jpi.2023.100190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Background GP63, also known as Leishmanolysin, is a multifunctional virulence factor abundant on the surface of Leishmania spp. small peptides with anticancer capabilities that are selective and toxic to cancer cells are known as anticancer peptides. We aimed to demonstrate the activity of GP63 and its anticancer properties on melanoma using a range of in silico tools and screening methods to identify predicted and designed anticancer peptides. Methods Various in silico modeling methodologies are used to establish the three-dimensional (3D) structure of GP63. Refinement and re-evaluation of the modeled structures and the built models' quality evaluated using the different docking used to find the interacting amino acids between MMP2 and GP63 and its anticancer peptides. AntiCP2.0 is used for screening anticancer peptides. 2D interaction plots of protein-ligand complexes evaluated by Protein-Ligand Interaction Profiler server. It is for the first time that used anticancer peptides of GP63 and the predicted and designed peptides. Results We used 3 peptides of GP63 based on the AntiCP 2.0 server with scores of 0.63, 0.53, and 0.49, and common peptides of GP63/MMP2 (continues peptide: mean the completely selected peptide after docking with non-anticancer effect, predicted with 0.58 score and designed peptides with 0.47 and 0.45 scores by AntiCP 2.0 server). Conclusions The antileishmanial and anticancer peptide research topics exemplify the multidisciplinary nature of peptide research. The advancement of therapeutics targeting cancer and/or Leishmania requires an interconnected research strategy shown in this work.
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Key Words
- ACPs, anticancer peptides
- Anticancer
- CASTp, Computed Atlas of Surface Topography of proteins
- CL, cutaneous leishmaniasis
- GP63, Glycoprotein 63
- In silico
- Leishmania
- Leishmanolysin
- MD, molecular dynamics
- MMPs, matrix metalloproteases
- MSP, major surface protease
- Matrix metalloproteases
- PDB, Protein Data Bank
- PLIP, Protein–Ligand Interaction Profiler
- Peptide
- Protein–Ligand Interaction Profiler
- ROS, reactive oxygen species formation
- SVM, Support Vector Machine
- VL, visceral leishmaniasis
- kNN, k-Nearest Neighbors
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Affiliation(s)
- Fatemeh Sharifi
- Research Center of Tropical and Infectious Diseases, Kerman University of Medical Sciences, Kerman, Iran
| | - Iraj Sharifi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Zahra Babaei
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Sodabeh Alahdin
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran,Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran,Corresponding author.
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Gaur V, Bera S. Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches. Curr Res Pharmacol Drug Discov 2022; 3:100137. [PMID: 36568273 PMCID: PMC9780078 DOI: 10.1016/j.crphar.2022.100137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/24/2022] [Revised: 10/09/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The rapid emergence of antibiotic resistance among various bacterial pathogens has been one of the major concerns of health organizations across the world. In this context, for the development of novel inhibitors against antibiotic-resistant bacterial pathogens, UDP-N-Acetylmuramoyl-L-Alanine-D-Glutamate Ligase (MurD) enzyme represents one of the most apposite targets. Body The present review focuses on updated advancements on MurD-targeted inhibitors in recent years along with genetic regulation, structural and functional characteristics of the MurD enzyme from various bacterial pathogens. A concise account of various crystal structures of MurD enzyme, submitted into Protein Data Bank is also discussed. Discussion MurD, an ATP dependent cytoplasmic enzyme is an important target for drug discovery. The genetic organization of MurD enzyme is well elucidated and many crystal structures of MurD enzyme are submitted into Protein Data bank. Various inhibitors against MurD enzyme have been developed so far with an increase in the use of in-silico methods in the recent past. But cell permeability barriers and conformational changes of MurD enzyme during catalytic reaction need to be addressed for effective drug development. So, a combination of in-silico methods along with experimental work is proposed to counter the catalytic machinery of MurD enzyme.
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Key Words
- Antibiotic resistance
- HTS, High Throughput Screening
- In-silico
- MD, Molecular Dynamics
- MIC, Minimum Inhibitory Concentration
- MurD
- PDB, Protein Data Bank
- PEP, Phosphoenolpyruvate
- PG, Peptidoglycan
- Peptidoglycan
- SAR, Structural Activity Relationship
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-Mpp, UDP-N-acetylmuramylpentapeptide
- UDP-MurNAc, UDP-N-acetylmuramicacid
- UMA, UDP N-acetylmuramoyl-l-alanine
- UNAG, UDP- N-acetylglucosamine
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Sarkar A, Agarwal R, Bandyopadhyay B. Molecular docking studies of phytochemicals from Terminalia chebula for identification of potential multi-target inhibitors of SARS-CoV-2 proteins. J Ayurveda Integr Med 2022;:100557. [PMID: 35185301 DOI: 10.1016/j.jaim.2022.100557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/10/2021] [Revised: 12/14/2021] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Background The COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a global pandemic claiming more than 6 million lives worldwide as of 16 March 2022. Till date, no medicine has been developed which is proved to have 100% efficiency in combating against this deadly disease. We focussed on ayurvedic medicines to identify drug-like candidates for treatment and management of COVID-19. Among all ayurvedic medicines, we were interested in Terminalia chebula (T. chebula), as it is known to have antibacterial, antifungal, antiviral, antioxidant and anti-inflammatory properties. Objectives In this study, we evaluated potential inhibitory effects of phytochemicals from T. chebula against eight structural and functional proteins of SARS-CoV-2. Material and methods We performed blind molecular docking studies using fifteen phytochemicals from T. chebula against the proteins of SARS-CoV-2. The three-dimensional proteins structures were analysed and potential drug-binding sites were identified. The drug-likeness properties of the ligands were assessed as well. Results Analysing the docking results by comparing Atomic Contact Energy (ACE) and intermolecular interactions along with assessment of ADME/T properties identified 1,3,6-Trigalloyl glucose (−332.14 ± 55.74 kcal/mol), Beta-Sitosterol (−324.75 ± 36.98 kcal/mol) and Daucosterol (−335.67 ± 104.79 kcal/mol) as most promising candidates which exhibit significantly high inhibition efficiency against all eight protein targets. Conclusions We believe that our study has the potential to help the scientific communities to develop multi-target drugs from T. chebula to combat against the deadly pathogen of COVID-19, with the support of extensive wet lab analysis.
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Fatima K, Masood N, Ahmad Wani Z, Meena A, Luqman S. Neomenthol prevents the proliferation of skin cancer cells by restraining tubulin polymerization and hyaluronidase activity. J Adv Res 2021; 34:93-107. [PMID: 35024183 DOI: 10.1016/j.jare.2021.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/12/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022] Open
Abstract
Introduction Neomenthol, a cyclic monoterpenoid, is a stereoisomer of menthol present in the essential oil of Mentha spp. It is used in food as a flavoring agent, in cosmetics and medicines because of its cooling effects. However, neomenthol has not been much explored for its anticancer potential. Additionally, targeting hyaluronidase, Cathepsin-D, and ODC by phytochemicals is amongst the efficient approach for cancer prevention and/or treatment. Objectives To investigate the molecular and cell target-based antiproliferative potential of neomenthol on human cancer (A431, PC-3, K562, A549, FaDu, MDA-MB-231, COLO-205, MCF-7, and WRL-68) and normal (HEK-293) cell lines. Methods The potency of neomenthol was evaluated on human cancer and normal cell line using SRB, NRU and MTT assays. The molecular target based study of neomenthol was carried out in cell-free and cell-based test systems. Further, the potency of neomenthol was confirmed by quantitative real-time PCR analysis and molecular docking studies. The in vivo anticancer potential of neomenthol was performed on mice EAC model and the toxicity examination was accomplished through in silico, ex vivo and in vivo approaches. Results Neomenthol exhibits a promising activity (IC50 17.3 ± 6.49 μM) against human epidermoid carcinoma (A431) cells by arresting the G2/M phase and increasing the number of sub-diploid cells. It significantly inhibits hyaluronidase activity (IC50 12.81 ± 0.01 μM) and affects the tubulin polymerization. The expression analysis and molecular docking studies support the in vitro molecular and cell target based results. Neomenthol prevents EAC tumor formation by 58.84% and inhibits hyaluronidase activity up to 10% at 75 mg/kg bw, i.p. dose. The oral dose of 1000 mg/kg bw was found safe in acute oral toxicity studies. Conclusion Neomenthol delayed the growth of skin carcinoma cells by inhibiting the tubulin polymerization and hyaluronidase activity, which are responsible for tumor growth, metastasis, and angiogenesis.
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Key Words
- AA, Arachidonic acid
- AKLP, Alkaline phosphatase
- Ab/Am, Antibiotic/antimycotic
- BE, Binding energy
- BIL, Bilirubin total & direct
- BSA, Bovine serum albumin
- BUN, Blood urea nitrogen
- CATD, Cathepsin D
- CHOL, Cholesterol
- CM-H2DCFDA, Chloromethyl derivative of dichloro fluorescin diacetate
- COX-2, Cyclooxygenase 2
- CRTN, Creatinine
- Cancer biomarker
- DCFDA, 2′,7′ dichloro fluorescin diacetate
- DFMO, α-difluoro methyl ornithine
- DHFR, Dihydrofolatereductase
- DMEM, Dulbecco’s minimal essential media
- DMSO, Dimethyl sulfoxide
- DNA, Deoxyribonucleic acid
- DOXO, Doxorubicin
- EAC, Ehlrich Ascites Carcinoma
- EC50, Half maximal effective concentration
- EDTA, Ethylene diamine tetra acetic acid
- ELISA, enzyme-linked immunosorbent assay
- Ehrlich Ascites Carcinoma
- FACS, Fluorescence-Activated Cell Sorting
- FBS, Fetal bovine serum
- FDA, Food and Drug Administration
- FOX, Ferrous oxidation-xylenol orange
- GAPDH, Glyceraldehyde 3-phosphate dehydrogenase, HEPES, N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid
- HA, Hyaluronic acid
- HDAC, Histone deacetylase
- HDL, High density lipoprotein
- HYAL, Hyaluronidase
- Human epidermoid carcinoma
- Hyaluronidase
- IC50, Half maximal inhibitory concentration
- IDT, Integrated DNA Technologies
- Ki, Inhibitory constant
- LDH, Lactate dehydrogenase
- LOX-5, Lipoxygenase-5
- MEF, Mean erythrocyte fragility
- MMP, Mitochondrial membrane potential
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- MTX, Methotrexate
- NAC, N-acetyl cysteine
- NADPH, Nicotinamide adenine dinucleotide phosphate hydrogen
- NRU, Neutral red uptake
- NaOH, Sodium hydroxide
- Neomenthol
- ODC, Ornithine decarboxylase
- OECD, Organization for Economic Co-operation and Development
- OF, Osmotic fragility
- PBS, Phosphate buffer saline
- PCR, Polymerase chain reaction
- PDB, Protein Data Bank
- PDT, Podophyllotoxin
- PEP A, pepstatin A
- PI, Propidium iodide
- PI3K, Phosphotidyl inositol-3 kinase
- PKB/Akt, Protein kinase B
- RBC, Red blood cell
- RIPA, Radio immune precipitation assay buffer
- RNA, Ribonucleic acid
- RNase A, Ribonuclease A
- ROS, Reactive oxygen species
- RPMI, Roswell park memorial institute
- Rh123, Rhodamine 123
- SGOT, Aspartate aminotransferase
- SGPT, Alanine aminotransferase
- SRB, Sulphorhodamine B
- TCA, Tricarboxylic acid
- TMPD, N,N,N′,N′-tetramethyl-p-phenylenediamine
- TNBS, Trinitrobenzenesulphonic acid
- TPA, 12-O-Tetradecanoylphorbol-13-acetate
- TPR, Total protein
- TRIG, Triglyceraldehyde
- TRPM8, Transient receptor potential member 8
- Tubulin
- URIC, Uric acid
- WBC, White blood cell
- mTOR, Mammalian target of rapamycin
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Zhdanova PV, Ishchenko AA, Chernonosov AA, Zharkov DO, Koval VV. Dataset for dynamics and conformational changes in human NEIL2 protein analyzed by integrative structural biology approach. Data Brief 2022; 40:107760. [PMID: 35005149 DOI: 10.1016/j.dib.2021.107760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/04/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
This work presents new data on human endonuclease VIII-like 2 protein (hNEIL2), a part of DNA glycosylases of the helix–two-turn–helix structural superfamily. While X-ray structure of oNEIL2 (opossum Monodelphis) was resolved partially [1], the structure of hNEIL2 has not yet been determined. This data article describes a powerful combination of hydrogen-deuterium exchange mass spectrometry, homology modeling, and molecular dynamics simulations for protein conformational dynamics analysis. The data supplied in this work are related to the research article entitled “Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry”.
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Key Words
- Base excision repair
- CD, circular dichroism
- DNA damage
- DNA glycosylases
- DNA repair
- DTT, (2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diol
- ESI, electrospray ionization
- HDX-MS
- HDX-MS, hydrogen-deuterium exchange mass spectrometry
- HEPES, 2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid
- IPTG, Propan-2-yl 1-thio-β-D-galactopyranoside
- LB, Lysogeny broth
- LC-MS, liquid chromatography–mass spectrometry
- MD, molecular dynamics
- MDTRA, Molecular Dynamics Trajectory Reader & Analyzer
- Molecular dynamics
- NEIL2
- PDB, Protein Data Bank
- RMSD, root-mean-square deviation
- SDS-PAGE, sodium dodecyl sulphate–polyacrylamide gel electrophoresis
- Structural dynamics
- TCEP, 3,3’,3’’-Phosphanetriyltripropanoic acid
- hNEIL2, human endonuclease VIII-like 2 protein
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Abstract
The ongoing pandemic of COVID-19 caused by the SARS-COV2 virus has triggered millions of deaths around the globe. Emerging several variants of the virus with increased transmissibility, the severity of disease, and the ability of the virus to escape from the immune system has a cause for concerns. Here, we compared the spike protein sequence of 91 human SARS CoV2 strains of Iraq to the first reported sequence of SARS-CoV2 isolate from Wuhan Hu-1/China. The strains were isolated between June 2020 and March 2021. Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S, D1118H. The most frequently mutations occurred at the D614G (87/91), followed by S982A (50/91), and A570D (48/91), respectively. In addition, a distinct shift was observed in the type of SARS-COV2 variants present in 2020 compared to 2021 isolates. In 2020, B.1.428.1 lineage was appeared to be a dominant variant (85%). However, the diversity of the variants increased in 2021, and the majority (73%) of the isolated were appeared to belong to B.1.1.7 lineage (VOC/alpha variants). To our knowledge, this is the first major genome analysis of SARS-CoV2 in Iraq. The data from this research could provide insights into SARS-CoV2 evolution, and can be potentially used to recognize the effective vaccine against the disease.
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Key Words
- ACE2, Angiotensin-Converting Enzyme 2
- CP, Cytoplasmic Peptide
- Covid-19
- FP, Fusion peptide
- GISAID, Global Initiative on Sharing All Influenza Data
- HR1, Heptad Repeat 1
- HR2, Heptad Repeat 2
- Iraq
- Mutation
- NTD, N-terminal domain
- PDB, Protein Data Bank
- RBD, Receptor-Binding Domain
- Receptor binding domain
- SARS-COV2
- SARS-CoV2, Severe acute respiratory syndrome coronavirus 2
- SP, Signal Peptide
- Spike protein
- TM, Transmembrane Domain
- VOC, Virus of Concern
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Affiliation(s)
- Dana Khdr Sabir
- Department of Medical Laboratory Sciences, College of Medical and Applied Sciences, Charmo University, 46023 Chamchamal, Kurdistan Region, Iraq
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Song S, Gao P, Sun L, Kang D, Kongsted J, Poongavanam V, Zhan P, Liu X. Recent developments in the medicinal chemistry of single boron atom-containing compounds. Acta Pharm Sin B 2021; 11:3035-3059. [PMID: 34729302 PMCID: PMC8546671 DOI: 10.1016/j.apsb.2021.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 11/03/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Various boron-containing drugs have been approved for clinical use over the past two decades, and more are currently in clinical trials. The increasing interest in boron-containing compounds is due to their unique binding properties to biological targets; for example, boron substitution can be used to modulate biological activity, pharmacokinetic properties, and drug resistance. In this perspective, we aim to comprehensively review the current status of boron compounds in drug discovery, focusing especially on progress from 2015 to December 2020. We classify these compounds into groups showing anticancer, antibacterial, antiviral, antiparasitic and other activities, and discuss the biological targets associated with each activity, as well as potential future developments.
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Key Words
- ACTs, artemisinin combination therapies
- ADCs, Acinetobacter-derived cephalosporinases
- AML, acute myeloid leukemia
- AMT, aminopterin
- BLs, β-lactamases
- BNCT, boron neutron capture therapy
- BNNPs, boron nitride nanoparticles
- BNNTs, boron nitride nanotubes
- Boron-containing compounds
- CEs, carboxylesterases
- CIA, collagen-induced arthritis
- COVID-19, coronavirus disease 2019
- ClpP, casein protease P
- Covalent inhibitors
- GSH, glutathione
- HADC1, class I histone deacetylase
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HIV, human immunodeficiency virus
- LeuRS, leucyl-tRNA synthetase
- Linker components
- MBLs, metal β-lactamases
- MDR-TB, multidrug-resistant tuberculosis
- MERS, Middle East respiratory syndrome
- MIDA, N-methyliminodiacetic acid
- MM, multiple myeloma
- MTX, methotrexate
- Mcl-1, myeloid cell leukemia 1
- Mtb, Mycobacterium tuberculosis
- NA, neuraminidase
- NS5B, non-nucleoside polymerase
- OBORT, oxaborole tRNA capture
- OPs, organophosphate
- PBA, phenylboronic acid
- PDB, Protein Data Bank
- PPI, protein–protein interaction
- Prodrug
- QM, quinone methide
- RA, rheumatoid arthritis
- ROS, reactive oxygen species
- SARS-CoV-2, syndrome coronavirus 2
- SBLs, serine β-lactamases
- SERD, selective estrogen receptor downregulator
- SHA, salicyl hydroxamic acid
- SaClpP, Staphylococcus aureus caseinolytic protease P
- TB, tuberculosis
- TTR, transthyretin
- U4CR, Ugi 4-component reaction
- cUTI, complex urinary tract infection
- dCTPase, dCTPase pyrophosphatase
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Affiliation(s)
- Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
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10
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Zhang L, Zhang L, Guo Y, Xiao M, Feng L, Yang C, Wang G, Ouyang L. MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. Acta Pharm Sin B 2021; 11:3092-104. [PMID: 34729303 DOI: 10.1016/j.apsb.2021.05.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 01/12/2021] [Revised: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 02/05/2023] Open
Abstract
Mitotic catastrophe (MC) is a form of programmed cell death induced by mitotic process disorders, which is very important in tumor prevention, development, and drug resistance. Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study, it is urgent for us to develop a professional and comprehensive database to curate MC-related data. Mitotic Catastrophe Database (MCDB) consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles. Also, MCDB defines the confidence level, classification criteria, and uniform naming rules for MC-related data, which greatly improves data reliability and retrieval convenience. Moreover, MCDB develops protein sequence alignment and target prediction functions. The former can be used to predict new potential MC-related genes and proteins, and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds. In short, MCDB is such a proprietary, standard, and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry, molecular biology, bioinformatics, oncology and so on. The MCDB is distributed on http://www.combio-lezhang.online/MCDB/index_html/.
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Key Words
- Data mining
- Database
- GO, Gene Ontology
- IUPAC, International Union of Pure and Applied Chemistry
- InChI Key, International Chemical Identifier hash
- InChI, International Chemical Identifier
- MC, Mitotic Catastrophe
- MCDB, Mitotic Catastrophe Database
- Mitotic catastrophe
- PDB, Protein Data Bank
- PMID, PubMed identifier
- Protein sequence analysis
- PubChem, Public Chemistry
- PubMed, Public Medicine
- SMILES, Simplified Molecular Input Line Entry Specification
- Target prediction
- UniProt, Universal Protein Resource
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11
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Wang Z, Yang L, Zhao XE. Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery. Comput Struct Biotechnol J 2021; 19:4684-4701. [PMID: 34426762 PMCID: PMC8373586 DOI: 10.1016/j.csbj.2021.08.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/28/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Safer and more-effective drugs are urgently needed to counter infections with the highly pathogenic SARS-CoV-2, cause of the COVID-19 pandemic. Identification of efficient inhibitors to treat and prevent SARS-CoV-2 infection is a predominant focus. Encouragingly, using X-ray crystal structures of therapeutically relevant drug targets (PLpro, Mpro, RdRp, and S glycoprotein) offers a valuable direction for anti-SARS-CoV-2 drug discovery and lead optimization through direct visualization of interactions. Computational analyses based primarily on MMPBSA calculations have also been proposed for assessing the binding stability of biomolecular structures involving the ligand and receptor. In this study, we focused on state-of-the-art X-ray co-crystal structures of the abovementioned targets complexed with newly identified small-molecule inhibitors (natural products, FDA-approved drugs, candidate drugs, and their analogues) with the assistance of computational analyses to support the precision design and screening of anti-SARS-CoV-2 drugs.
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Key Words
- 3CLpro, 3C-Like protease
- ACE2, angiotensin-converting enzyme 2
- COVID-19, coronavirus disease 2019
- Candidate drugs
- Co-crystal structures
- DyKAT, dynamic kinetic asymmetric transformation
- EBOV, Ebola virus
- EC50, half maximal effective concentration
- EMD, Electron Microscopy Data
- FDA, U.S. Food and Drug Administration
- FDA-approved drugs
- HCoV-229E, human coronavirus 229E
- HPLC, high-performance liquid chromatography
- IC50, half maximal inhibitory concentration
- MD, molecular dynamics
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MMPBSA, molecular mechanics Poisson-Boltzmann surface area
- MTase, methyltransferase
- Mpro, main protease
- Natural products
- Nsp, nonstructural protein
- PDB, Protein Data Bank
- PLpro, papain-like protease
- RTP, ribonucleoside triphosphate
- RdRp, RNA-dependent RNA polymerase
- SAM, S-adenosylmethionine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SI, selectivity index
- Ugi-4CR, Ugi four-component reaction
- cryo-EM, cryo-electron microscopy
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
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12
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Quadros Gomes AR, da Rocha Galucio NC, de Albuquerque KCO, Brígido HPC, Varela ELP, Castro ALG, Vale VV, Bahia MO, Rodriguez Burbano RM, de Molfeta FA, Carneiro LA, Percario S, Dolabela MF. Toxicity evaluation of Eleutherine plicata Herb. extracts and possible cell death mechanism. Toxicol Rep 2021; 8:1480-1487. [PMID: 34401358 PMCID: PMC8353407 DOI: 10.1016/j.toxrep.2021.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/04/2021] [Revised: 07/05/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023] Open
Abstract
Ethanol extract of Eleutherine plicata showed low in vitro and in vivo cytotoxic potential. The dichloromethane fraction was cytotoxic to HepG2 and caused DNA. However, no toxicity was observed in vivo. Isoeleutherin caused DNA damage by the comet method and activated caspase-8 in the in silico study.
Eleutherine plicata has been shown to be a promising medicinal plant, and its activity has been associated with naphthoquinones. The present study aimed at evaluating the cytotoxicity, genotoxicity, and oral toxicity of the ethanol extract (EEEp), dichloromethane fraction (FDMEp) of E. plicata, and isoeleutherin. For the cytotoxicity evaluation, the viability test (MTT) was used. Genotoxicity was accessed through the Comet assay (alkaline version), acute and subacute oral toxicities were also evaluated. The antioxidant capacity of the samples in the wells where the cells were treated with E. plicata was evaluated. Furthermore, the participation of caspase-8 in the possible mechanism of action of isoeleutherin, eleutherin, and eleutherol was also investigated through a docking study. FDMEp and isoeleutherin were cytotoxic, with higher rates of DNA fragmentation observed for FDMEp and isoeleutherin, and all samples displayed higher antioxidant potential than the control. In the acute oral toxicity test, EEEp, FDMEp, and isoeleutherin did not cause significant clinical changes. In the subacute toxicity assay, EEEp and FDMEp also did not cause clinical, hematological, or biochemical changes. The three compounds bound similarly to caspase-8. Despite the results of cytotoxicity, in vitro studies demonstrated that the use of EEEp appears to be safe and cell death may involve its binding to caspase-8.
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Key Words
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- BCRJ, Cell bank of Rio de Janeiro
- BFS, bovine fetal serum
- Caspase-8
- DARP, dopamine releasing protein
- DMEM, Dulbecco's Modified Eagle's Medium
- DMSO, dimethyl sulfoxide
- DPPH, 2,2-diphenyl-1-picrylhydrazyl
- EDTA, ethylenediaminetetraacetic
- EEEp, ethanol extract of Eleutherine plicata
- Eleutherin
- Eleutherine plicata
- Eleutherol
- FADD, Fas associated death domain
- FDMEp, dichloromethane fraction of Eleutherine plicata
- FrAE, ethyl acetate fraction of Elutherine plicata
- GA, Genetic Algorithm
- GOLD, Genetic Optimization for Ligand Docking
- HPLC, high performance liquid chromatography
- IC50, 50 % cytotoxic concentration
- Isoeleutherin
- MD, molecular dynamics
- MTT, ([3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide])
- NMR, nuclear magnetic resonance
- NMU, N-methyl-N-nitrosurea
- OECD, Organization for Economic Co-Operation and Development
- PDB, Protein Data Bank
- ROS, reactive oxygen species
- RPMI, Roswell Park Memorial Institute medium
- RSMD, root mean square deviation
- TLC, tin layer chromatography
- TNFR, tumour necrosis fator receptor
- Toxicity
- rpm, rotations per minute
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Affiliation(s)
- Antonio Rafael Quadros Gomes
- Postgraduate Program in Pharmaceutical Innovation, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Natasha Costa da Rocha Galucio
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Postgraduate Program in Pharmaceutical Sciences, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | | | - Heliton Patrick Cordovil Brígido
- Postgraduate Program in Pharmaceutical Innovation, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Everton Luiz Pompeu Varela
- Postgraduate Program in Biodiversity and Biotechnology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Oxidative Stress Research Laboratory, Institute of Biological Sciences, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Ana Laura Gadelha Castro
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Valdicley Vieira Vale
- Postgraduate Program in Pharmaceutical Innovation, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Marcelo Oliveira Bahia
- Postgraduate Program in Neuroscience and Cell Biology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Rommel Mario Rodriguez Burbano
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Postgraduate Program in Neuroscience and Cell Biology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Fábio Alberto de Molfeta
- Postgraduate Program in Chemistry, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | | | - Sandro Percario
- Postgraduate Program in Biodiversity and Biotechnology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Oxidative Stress Research Laboratory, Institute of Biological Sciences, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
| | - Maria Fâni Dolabela
- Postgraduate Program in Pharmaceutical Innovation, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Postgraduate Program in Pharmaceutical Sciences, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil.,Postgraduate Program in Biodiversity and Biotechnology, Federal University of Pará, Av. Augusto Corrêa, 1, Guamá, 66075-110, Belém, PA, Brazil
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13
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Itoh T, Yaguchi M, Nakaichi A, Yoda M, Hibi T, Kimoto H. Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/ N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. J Struct Biol X 2021; 5:100049. [PMID: 34195603 PMCID: PMC8233162 DOI: 10.1016/j.yjsbx.2021.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 10/27/2022]
Abstract
The chitinolytic bacterium Paenibacillus sp. str. FPU-7 efficiently degrades chitin into oligosaccharides such as N-acetyl-D-glucosamine (GlcNAc) and disaccharides (GlcNAc)2 through multiple secretory chitinases. Transport of these oligosaccharides by P. str. FPU-7 has not yet been clarified. In this study, we identified nagB1, predicted to encode a sugar solute-binding protein (SBP), which is a component of the ABC transport system. However, the genes next to nagB1 were predicted to encode two-component regulatory system proteins rather than transmembrane domains (TMDs). We also identified nagB2, which is highly homologous to nagB1. Adjacent to nagB2, two genes were predicted to encode TMDs. Binding experiments of the recombinant NagB1 and NagB2 to several oligosaccharides using differential scanning fluorimetry and surface plasmon resonance confirmed that both proteins are SBPs of (GlcNAc)2 and (GlcNAc)3. We determined their crystal structures complexed with and without chitin oligosaccharides at a resolution of 1.2 to 2.0 Å. The structures shared typical SBP structural folds and were classified as subcluster D-I. Large domain motions were observed in the structures, suggesting that they were induced by ligand binding via the "Venus flytrap" mechanism. These structures also revealed chitin oligosaccharide recognition mechanisms. In conclusion, our study provides insight into the recognition and transport of chitin oligosaccharides in bacteria.
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Key Words
- ABC transporter
- ABC, ATP-binding cassette
- Chitin oligosaccharide
- DSF, differential scanning fluorimetry
- GH, glycoside hydrolase
- GlcN, D-glucosamine
- GlcNAc, N-acetyl-D-glucosamine
- OD600, optical density at 600 nm
- PDB, Protein Data Bank
- PTS, phosphoenolpyruvate phosphotransferase system
- Paenibacillus
- RU, response unit
- SBP, solute binding protein
- Se-Met, selenomethionine
- Solute binding protein
- TMD, transmembrane domain
- Two-component regulatory system
- a.a., amino acid
- r.m.s.d., root mean-square deviation
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Misaki Yaguchi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Akari Nakaichi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Moe Yoda
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
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14
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Alterio V, Langella E, Buonanno M, Esposito D, Nocentini A, Berrino E, Bua S, Polentarutti M, Supuran CT, Monti SM, De Simone G. Zeta-carbonic anhydrases show CS 2 hydrolase activity: A new metabolic carbon acquisition pathway in diatoms? Comput Struct Biotechnol J 2021; 19:3427-3436. [PMID: 34194668 PMCID: PMC8217695 DOI: 10.1016/j.csbj.2021.05.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022] Open
Abstract
CDCA1 is a carbonic anhydrase that can utilize Zn(II) or Cd(II) as catalytic metal. CDCA1 has been the first enzyme to show an efficient utilization of Cd(II) ions in Nature. By using a multidisciplinary approach, we discovered that CS2 is a substrate for this enzyme. CDCA1 is the unique enzyme, known so far, able to use both CS2 and CO2 as substrates.
CDCA1 is a very peculiar member of the Carbonic Anhydrase (CA) family. It has been the first enzyme to show an efficient utilization of Cd(II) ions in Nature and a unique adaptation capability to live on the surface ocean. Indeed, in this environment, which is extremely depleted in essential metal ions, CDCA1 can utilize Zn(II) or Cd(II) as catalytic metal to support the metabolic needs of fast growing diatoms. In this paper we demonstrate a further catalytic versatility of this enzyme by using a combination of X-ray crystallography, molecular dynamics simulations and enzymatic experiments. First we identified the CO2 binding site and the way in which this substrate travels from the environment to the enzyme active site. Then, starting from the observation of a structural similarity with the substrate entry route of CS2 hydrolase from Acidanius A1-3, we hypothesized and demonstrated that also CS2 is a substrate for CDCA1. This finding is new and unexpected since until now only few CS2 hydrolases have been characterized, and none of them is reported to have any CO2 hydratase action. The physiological implications of this supplementary catalytic activity still remain to be unveiled. We suggest here that it could represent another ability of diatoms expressing CDCA1 to adapt to the external environment. Indeed, the ability of this enzyme to convert CS2 could represent an alternative source of carbon acquisition for diatoms, in addition to CO2.
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Key Words
- AAZ, Acetazolamide
- CA, Carbonic Anhydrase
- CAI, Carbonic Anhydrase Inhibitor
- CCD, Charge Coupled Device
- CDCA1, Cadmium-specific Carbonic Anhydrase
- CO2
- CS2
- CS2H, S. solfataricus CS2 hydrolase
- Cambialistic enzyme
- Carbonic Anhydrase
- DMSO, Dimethyl Sulfoxide
- FbiCA, Flaveria bidentis Carbonic Anhydrase
- HEPES, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- MD, Molecular Dynamics
- Molecular dynamics
- NCS, Non-Crystallographic Symmetry
- PDB, Protein Data Bank
- PEG, Polyethylene glycol
- SDS-PAGE, Sodium Dodecyl Sulphate - PolyAcrylamide Gel Electrophoresis
- Tris-HCl, Tris(hydroxymethyl)aminomethane hydrochloride
- bCA, bovine Carbonic Anhydrase
- hCA, human Carbonic Anhydrase
- psCA3, Pseudomonas aeruginosa Carbonic Anhydrase 3
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Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Emma Langella
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Martina Buonanno
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Davide Esposito
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Emanuela Berrino
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Silvia Bua
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Maurizio Polentarutti
- Elettra - Sincrotrone Trieste, s.s. 14 Km 163.5 in Area Science Park, Basovizza (Trieste) 34149, Trieste, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
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Jain AS, Sushma P, Dharmashekar C, Beelagi MS, Prasad SK, Shivamallu C, Prasad A, Syed A, Marraiki N, Prasad KS. In silico evaluation of flavonoids as effective antiviral agents on the spike glycoprotein of SARS-CoV-2. Saudi J Biol Sci 2021; 28:1040-1051. [PMID: 33424398 PMCID: PMC7783825 DOI: 10.1016/j.sjbs.2020.11.049] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [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: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/02/2023] Open
Abstract
The novel coronavirus pandemic has spread over in 213 countries as of July 2020. Approximately 12 million people have been infected so far according to the reports from World Health Organization (WHO). Preventive measures are being taken globally to avoid the rapid spread of virus. In the current study, an in silico approach is carried out as a means of inhibiting the spike protein of the novel coronavirus by flavonoids from natural sources that possess both antiviral and anti-inflammatory properties. The methodology is focused on molecular docking of 10 flavonoid compounds that are docked with the spike protein of SARS-CoV-2, to determine the highest binding affinity at the binding site. Molecular dynamics simulation was carried out with the flavonoid-protein complex showing the highest binding affinity and highest interactions. The flavonoid naringin showed the least binding energy of -9.8 Kcal/mol with the spike protein which was compared with the standard drug, dexamethasone which is being repurposed to treat critically ill patients. MD simulation was carried out on naringin-spike protein complex for their conformational stability in the active site of the novel coronavirus spike protein. The RMSD of the complex appeared to be more stable when compared to that of the protein from 0.2 nm to 0.4 nm. With the aid of this in silico approach further in vitro studies can be carried out on these flavonoids against the novel coronavirus as a means of viral protein inhibitors.
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Affiliation(s)
- Anisha S. Jain
- Department of Microbiology , School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - P. Sushma
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Chandan Dharmashekar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Mallikarjun S. Beelagi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Shashanka K. Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Ashwini Prasad
- Department of Microbiology , School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka 570 015, India
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Najat Marraiki
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Kollur Shiva Prasad
- Department of Sciences, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka 570 026, India
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16
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Alexandris N, Lagoumintzis G, Chasapis CT, Leonidas DD, Papadopoulos GE, Tzartos SJ, Tsatsakis A, Eliopoulos E, Poulas K, Farsalinos K. Nicotinic cholinergic system and COVID-19: In silico evaluation of nicotinic acetylcholine receptor agonists as potential therapeutic interventions. Toxicol Rep 2020; 8:73-83. [PMID: 33425684 PMCID: PMC7776751 DOI: 10.1016/j.toxrep.2020.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection was announced as a pandemic in March 2020. Since then, several scientists have focused on the low prevalence of smokers among hospitalized COVID-19 patients. These findings led to our hypothesis that the Nicotinic Cholinergic System (NCS) plays a crucial role in the manifestation of COVID-19 and its severe symptoms. Molecular modeling revealed that the SARS-CoV-2 Spike glycoprotein might bind to nicotinic acetylcholine receptors (nAChRs) through a cryptic epitope homologous to snake toxins, substrates well documented and known for their affinity to the nAChRs. This binding model could provide logical explanations for the acute inflammatory disorder in patients with COVID-19, which may be linked to severe dysregulation of NCS. In this study, we present a series of complexes with cholinergic agonists that can potentially prevent SARS-CoV-2 Spike glycoprotein from binding to nAChRs, avoiding dysregulation of the NCS and moderating the symptoms and clinical manifestations of COVID-19. If our hypothesis is verified by in vitro and in vivo studies, repurposing agents currently approved for smoking cessation and neurological conditions could provide the scientific community with a therapeutic option in severe COVID-19.
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Key Words
- ACh, Acetylcholine
- AChBP, Acetylcholine-binding protein
- ARDS, acute respiratory distress syndrome
- BLAST, Basic Local Alignment Search Tool
- CHARMM, Chemistry at Harvard Macromolecular Mechanics
- CNS, Central Nervous System
- COVID-19
- Cholinergic agonists
- CoV, coronavirus
- DCD, single precision binary FORTRAN
- ECD, extracellular domain
- HADDOCK, High Ambiguity Driven protein-protein DOCKing
- HMGB1, High-mobility group protein 1
- IL, Interleukin
- Jak2, Janus kinases 2
- LBD, Ligand Binding Domain
- MD, Molecular Dynamics
- MDS, Molecular Dynamics Simulations
- MERS, Middle East Respiratory Syndrome
- NAMD, Nanoscale Molecular Dynamics
- NCBI, National Center for Biotechnology Information
- NCS, Nicotinic Cholinergic System
- NF-kB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NPT, constant number, pressure, energy
- NVT, constant number, volume, energy
- Nicotinic acetylcholine receptors
- PDB, Protein Data Bank
- PME, Particle Mesh Ewald
- PRODIGY, PROtein binDIng enerGY prediction
- PyMOL, Python Molecule
- RBD, Receptor Binding Domain
- RMSD, Root-mean-square deviation
- SARS, Severe Acute Respiratory Syndrome
- SARS-CoV-2
- SARS-CoV-2 S1, SARS - 2 Spike Subunit 1 protein
- STAT3, signal transducer and activator of transcription 3
- STD NMR, Saturation Transfer Difference Nuclear Magnetic Resonance
- Spike glycoprotein
- TNF, Tumor Necrosis Factor
- VMD, Visual Molecular Dynamics
- lig, ligand
- nAChRs, nicotinic acetylcholine receptors
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Affiliation(s)
- Nikolaos Alexandris
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - George Lagoumintzis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Christos T. Chasapis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - Demetres D. Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Georgios E. Papadopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | | | | | - Elias Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantinos Poulas
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Konstantinos Farsalinos
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
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Megta AK, Pratap S, Kant A, Palva A, von Ossowski I, Krishnan V. Crystal structure of the atypically adhesive SpaB basal pilus subunit: Mechanistic insights about its incorporation in lactobacillar SpaCBA pili. Curr Res Struct Biol 2020; 2:229-238. [PMID: 34235482 PMCID: PMC8244301 DOI: 10.1016/j.crstbi.2020.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/27/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
To successfully colonize a host or environment, certain genera and species of Gram-positive bacteria have evolved to utilize the so-called sortase-dependent pilus, a long multi-subunit and non-flagellar surface adhesin. One example of this is Lactobacillus rhamnosus GG, a gut-adapted probiotic strain that produces SpaCBA pili. These structures are covalent hetero-oligomers built from three types of pilin subunit, each with a specific location and function (i.e., backbone SpaA for length, tip SpaC for adhesion, and basal SpaB for anchoring). Functionally, the SpaCBA pilus exhibits a promiscuous affinity for components on intestinal surfaces (e.g., mucus, collagen, and epithelial cells), which is largely attributed to the SpaC subunit. Then again, the basal SpaB pilin, in addition to acting as the terminal subunit during pilus assembly, displays an out of character mucoadhesive function. To address the structural basis of this unusual dual functionality, we reveal the 2.39 Å resolution crystal structure of SpaB. SpaB consists of one immunoglobulin-like CnaB domain and contains a putative intermolecular isopeptide bond-linking lysine and internal isopeptide bond-asparagine in an FPKN pilin motif within the C-terminal end. Remarkably, we found that a C-terminal stretch of positively charged lysine and arginine residues likely accounts for the atypical mucoadhesiveness of SpaB. Although harboring an autocatalytic triad of residues for a potential internal isopeptide interaction, the SpaB crystal structure lacked the visible electron density for intact bond formation, yet its presence was subsequently confirmed by mass spectral analysis. Finally, we propose a structural model that captures the exclusive basal positioning of SpaB in the SpaCBA pilus.
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Key Words
- ABC, ammonium bicarbonate
- ACN, acetonitrile
- Cell-wall anchoring
- Cna, collagen adhesin
- ECM, extracellular matrix
- Ig, immunoglobulin
- Lactobacillus rhamnosus GG
- MD, molecular dynamics
- MS, mass spectrometry
- Mucus adhesion
- PDB, Protein Data Bank
- PEG, polyethylene glycol
- Probiotic
- Sortase-dependent SpaCBA pili
- SpaB basal pilin
- rmsd, root mean square deviation
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Affiliation(s)
- Abhin Kumar Megta
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.,School of Biotechnology, KIIT University, Odisha, 751024, India
| | - Shivendra Pratap
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Abhiruchi Kant
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.,Department of Biotechnology, Manipal University, Karnataka, 576104, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Ingemar von Ossowski
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
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18
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Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020; 19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023] Open
Abstract
Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.
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Key Words
- CLEM, correlated light and electron microscopy
- Crosslinking mass spectrometry
- Cryo-electron microscopy
- Cryo-electron tomography
- EPR, electron paramagnetic resonance
- FRET, Forster resonance energy transfer
- ISB, Integrative structural biology
- Integrative structural biology
- ML, machine learning
- MR, molecular replacement
- MSAs, multiple sequence alignments
- MX, macromolecular crystallography
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Protein docking
- Protein structure prediction
- Quinary interactions
- SAD, single-wavelength anomalous dispersion
- SANS, small angle neutron scattering
- SAXS, small angle X-ray scattering
- X-ray crystallography
- XL-MS, cross-linking mass spectrometry
- cryo-EM SPA, cryo-EM single particle analysis
- cryo-EM, cryo-electron microscopy
- cryo-ET, cryo-electron tomography
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Affiliation(s)
- Samantha J. Ziegler
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Sam J.B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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Trigueiro-Louro J, Correia V, Figueiredo-Nunes I, Gíria M, Rebelo-de-Andrade H. Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike. Comput Struct Biotechnol J 2020; 18:2117-2131. [PMID: 32913581 PMCID: PMC7452956 DOI: 10.1016/j.csbj.2020.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 06/04/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
There are no approved target therapeutics against SARS-CoV-2 or other beta-CoVs. The beta-CoV Spike protein is a promising target considering the critical role in viral infection and pathogenesis and its surface exposed features. We performed a structure-based strategy targeting highly conserved druggable regions resulting from a comprehensive large-scale sequence analysis and structural characterization of Spike domains across SARSr- and MERSr-CoVs. We have disclosed 28 main consensus druggable pockets within the Spike. The RBD and SD1 (S1 subunit); and the CR, HR1 and CH (S2 subunit) represent the most promising conserved druggable regions. Additionally, we have identified 181 new potential hot spot residues for the hSARSr-CoVs and 72 new hot spot residues for the SARSr- and MERSr-CoVs, which have not been described before in the literature. These sites/residues exhibit advantageous structural features for targeted molecular and pharmacological modulation. This study establishes the Spike as a promising anti-CoV target using an approach with a potential higher resilience to resistance development and directed to a broad spectrum of Beta-CoVs, including the new SARS-CoV-2 responsible for COVID-19. This research also provides a structure-based rationale for the design and discovery of chemical inhibitors, antibodies or other therapeutic modalities successfully targeting the Beta-CoV Spike protein.
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Key Words
- ACE2, angiotensin-converting enzyme2
- Bat-SL-CoVs, bat SARS-like coronavirus
- Beta-CoVs, betacoronavirus
- Betacoronavirus
- CC, conserved cluster
- CD, connector domain
- CDP, consensus druggable pocket
- CDR, consensus druggable residue
- CH, central helix
- CP, cytoplasmic domain
- CR, connecting region
- CS, conservation score
- CoVs, coronavirus
- Coronavirus disease
- DGSS, DoGSiteScorer
- DPP4, dipeptidyl peptidase-4
- Druggability prediction
- FP, fusion peptide
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- MERS-CoVs, middle east respiratory syndrome coronavirus
- MERSr-CoVs, middle east respiratory syndrome-related coronavirus
- MSA, multiple sequence alignment
- NTD, N-terminal domain
- Novel antiviral targets
- PDB, Protein Data Bank
- PDS, PockDrug-Server
- RBD, Receptor-Binding Domain
- S, Spike
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SARS-CoVs, severe acute respiratory syndrome coronavirus
- SARSr-CoVs, severe acute respiratory syndrome-related coronavirus
- SD1, subdomain 1
- SD2, subdomain 2
- SF, SiteFinder from MOE
- SP, small pocket
- Sequence conservation
- Spike protein
- Sv, shorter variant
- T-RHS, top-ranked hot spots
- TMPRSS2, transmembrane protease serine 2
- aa, amino acid
- hSARSr-CoVs, human Severe acute respiratory syndrome-related coronavirus
- nts, nucleotides
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Affiliation(s)
- João Trigueiro-Louro
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Inês Figueiredo-Nunes
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Marta Gíria
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Helena Rebelo-de-Andrade
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
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20
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Bratty MA. Spectroscopic and molecular docking studies for characterizing binding mechanism and conformational changes of human serum albumin upon interaction with Telmisartan. Saudi Pharm J 2020; 28:729-736. [PMID: 32550805 PMCID: PMC7292872 DOI: 10.1016/j.jsps.2020.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/18/2020] [Accepted: 04/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human serum albumin (HSA), one of the most copious plasma proteins is responsible for binding and transportation of many exogenous and endogenous ligands including drugs. In this study, we intended to explore the extent and types of binding interaction present between HSA and the antihypertensive drug, telmisartan (TLM). The conformational changes in HSA due to this binding were also studied using different spectroscopic and molecular docking techniques. The spectral shifting and intensity variations upon interaction with TLM were studied using FT-IR spectroscopy. Binding constant and the change in absorption of HSA at its λmax was analyzed using absorption spectroscopy. Eventually, the types and extent of binding interactions were confirmed using molecular docking technique. Results have shown that TLM significantly interacts with the binding site-1 of HSA utilizing strong hydrogen bonding with Glu292, and Lys195 residues. The UV-absorption intensities were found to be decreased serially as the drug concentration increased with a binding constant of 1.01 × 103 M−1. The secondary structure analysis using FT-IR spectroscopy also revealed a marked reduction in the α-helix (56%) component of HSA on interaction. This study gives critical insights into the interaction of TLM with HSA protein which eventually affects the concentration of TLM reaching the site of action and ultimately its therapeutic profile.
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Key Words
- ADME, Absorption, Distribution, Metabolism, Excretion
- Binding
- FT-IR
- Glu, Glutamate
- HAS, Human Serum Albumin
- Human serum albumin
- Lys, Lysine
- Molecular Docking
- PDB, Protein Data Bank
- TLM, Telmisartan
- Telmisartan
- UCSF, University of California, San Fransisco
- UV–Vis
- λmax, wavelength of maximum absorbance
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Affiliation(s)
- Mohammed Al Bratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P. Box No. 114, Jazan, Saudi Arabia
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21
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Grobben Y, Uitdehaag JC, Willemsen-Seegers N, Tabak WW, de Man J, Buijsman RC, Zaman GJ. Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158. J Struct Biol X 2019; 4:100014. [PMID: 32647818 PMCID: PMC7337048 DOI: 10.1016/j.yjsbx.2019.100014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 10/19/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023]
Abstract
Arginase-1 is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine into L-ornithine and urea. Arginase-1 is abundantly expressed by tumor-infiltrating myeloid cells that promote tumor immunosuppression, which is relieved by inhibition of Arginase-1. We have characterized the potencies of the Arginase-1 reference inhibitors (2S)-2-amino-6-boronohexanoic acid (ABH) and N ω-hydroxy-nor-L-arginine (nor-NOHA), and studied their pH-dependence and binding kinetics. To gain a better understanding of the structural changes underlying the high pH optimum of Arginase-1 and its pH-dependent inhibition, we determined the crystal structure of the human Arginase-1/ABH complex at pH 7.0 and 9.0. These structures revealed that at increased pH, the manganese cluster assumes a more symmetrical coordination structure, which presumably contributes to its increase in catalytic activity. Furthermore, we show that binding of ABH involves the presence of a sodium ion close to the manganese cluster. We also studied the investigational new drug CB-1158 (INCB001158). This inhibitor has a low-nanomolar potency at pH 7.4 and increases the thermal stability of Arginase-1 more than ABH and nor-NOHA. Moreover, CB-1158 displays slow association and dissociation kinetics at both pH 9.5 and 7.4, as indicated by surface plasmon resonance. The potent character of CB-1158 is presumably due to its increased rigidity compared to ABH as well as the formation of an additional hydrogen-bond network as observed by resolution of the Arginase-1/CB-1158 crystal structure.
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Key Words
- ABH, (2S)-2-amino-6-boronohexanoic acid
- Biochemical inhibition
- Cancer immunotherapy
- DMSO, dimethyl sulfoxide
- IC50, half-maximal inhibitory concentration
- ITC, isothermal titration calorimetry
- KD, binding affinity
- KM, Michaelis constant
- Ki, inhibition constant
- MQ, MilliQ water
- PDB, Protein Data Bank
- RMSD, root-mean-square deviation
- SD, standard deviation
- SPR, surface plasmon resonance
- Surface plasmon resonance
- Thermal stability
- Tm, melting temperature
- X-ray crystallography
- ka, association rate constant
- kcat, catalytic rate constant
- kd, dissociation rate constant
- nor-NOHA, Nω-hydroxy-nor-L-arginine
- ΔTm, melting temperature shift
- τ, target residence time
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Abdelfatah S, Berg A, Huang Q, Yang LJ, Hamdoun S, Klinger A, Greten HJ, Fleischer E, Berg T, Wong VK, Efferth T. MCC1019, a selective inhibitor of the Polo-box domain of Polo-like kinase 1 as novel, potent anticancer candidate. Acta Pharm Sin B 2019; 9:1021-1034. [PMID: 31649851 PMCID: PMC6804483 DOI: 10.1016/j.apsb.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 08/23/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 01/01/2023] Open
Abstract
Polo-like kinase (PLK1) has been identified as a potential target for cancer treatment. Although a number of small molecules have been investigated as PLK1 inhibitors, many of which showed limited selectivity. PLK1 harbors a regulatory domain, the Polo box domain (PBD), which has a key regulatory function for kinase activity and substrate recognition. We report on 3-bromomethyl-benzofuran-2-carboxylic acid ethyl ester (designated: MCC1019) as selective PLK1 inhibitor targeting PLK1 PBD. Cytotoxicity and fluorescence polarization-based screening were applied to a library of 1162 drug-like compounds to identify potential inhibitors of PLK1 PBD. The activity of compound MC1019 against the PLK1 PBD was confirmed using fluorescence polarization and microscale thermophoresis. This compound exerted specificity towards PLK1 over PLK2 and PLK3. MCC1019 showed cytotoxic activity in a panel of different cancer cell lines. Mechanistic investigations in A549 lung adenocarcinoma cells revealed that MCC1019 induced cell growth inhibition through inactivation of AKT signaling pathway, it also induced prolonged mitotic arrest—a phenomenon known as mitotic catastrophe, which is followed by immediate cell death via apoptosis and necroptosis. MCC1019 significantly inhibited tumor growth in vivo in a murine lung cancer model without affecting body weight or vital organ size, and reduced the growth of metastatic lesions in the lung. We propose MCC1019 as promising anti-cancer drug candidate.
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Key Words
- 3-MA, 3-methyladenine
- ABC, avidin-biotin complex
- APC/C, anaphase-promoting complex/cyclosome
- BUBR1, budding uninhibited by benzimidazole-related 1
- CDC2, cell division cycle protein 2 homolog
- CDC25, cell division cycle 25
- CDK, cyclin-dependent kinase
- Cell cycle
- DAPI, 4′,6-diamidino-2-phenylindole
- DAPKs, death-associated protein kinase
- FBS, fetal bovine serum
- FOXO, forkhead box O
- HIF-1α, hypoxia-inducible factor 1 α
- IC50, 50% inhibition concentration
- IHC, immunohistochemistry
- Kd, the dissociation constant
- LC3, light chain 3
- MFP, M phase promoting factor
- MST, microscale thermophoresis
- MTD, maximal tolerance dose
- Mono-targeted therapy
- Nec-1, necrostatin 1
- Necroptosis
- PARP-1, poly(ADP-ribose) polymerase-1
- PBD, Polo box domain
- PDB, Protein Data Bank
- PI, propidium iodide
- PLK1
- PLK1, Polo-like kinase
- Polo box domain
- Polo-like kinase
- SAC, spindle assembly checkpoint
- Spindle damage
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Affiliation(s)
- Sara Abdelfatah
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
| | - Angela Berg
- Leipzig University, Institute of Organic Chemistry, Leipzig 04103, Germany
| | - Qi Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Li Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Sami Hamdoun
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
| | | | - Henry J. Greten
- Abel Salazar Institute of Biomedical Sciences, University of Porto, Porto 4099-003, Portugal
| | | | - Thorsten Berg
- Leipzig University, Institute of Organic Chemistry, Leipzig 04103, Germany
| | - Vincent K.W. Wong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
- Corresponding author. Tel.: +49 6131 3925751; fax: +49 6131 23752.
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23
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Picón-Pagès P, Bonet J, García-García J, Garcia-Buendia J, Gutierrez D, Valle J, Gómez-Casuso CE, Sidelkivska V, Alvarez A, Perálvarez-Marín A, Suades A, Fernàndez-Busquets X, Andreu D, Vicente R, Oliva B, Muñoz FJ. Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease. Comput Struct Biotechnol J 2019; 17:963-971. [PMID: 31360335 PMCID: PMC6639691 DOI: 10.1016/j.csbj.2019.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 01/18/2019] [Revised: 06/03/2019] [Accepted: 06/13/2019] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of extracellular deposits of amyloid β-peptide (Aβ), which induces neuronal death. Monomeric Aβ is not toxic but tends to aggregate into β-sheets that are neurotoxic. Therefore to prevent or delay AD onset and progression one of the main therapeutic approaches would be to impair Aβ assembly into oligomers and fibrils and to promote disaggregation of the preformed aggregate. Albumin is the most abundant protein in the cerebrospinal fluid and it was reported to bind Aβ impeding its aggregation. In a previous work we identified a 35-residue sequence of clusterin, a well-known protein that binds Aβ, that is highly similar to the C-terminus (CTerm) of albumin. In this work, the docking experiments show that the average binding free energy of the CTerm-Aβ1-42 simulations was significantly lower than that of the clusterin-Aβ1-42 binding, highlighting the possibility that the CTerm retains albumin's binding properties. To validate this observation, we performed in vitro structural analysis of soluble and aggregated 1 μM Aβ1-42 incubated with 5 μM CTerm, equimolar to the albumin concentration in the CSF. Reversed-phase chromatography and electron microscopy analysis demonstrated a reduction of Aβ1-42 aggregates when the CTerm was present. Furthermore, we treated a human neuroblastoma cell line with soluble and aggregated Aβ1-42 incubated with CTerm obtaining a significant protection against Aβ-induced neurotoxicity. These in silico and in vitro data suggest that the albumin CTerm is able to impair Aβ aggregation and to promote disassemble of Aβ aggregates protecting neurons.
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Key Words
- AD, Alzheimer's disease
- APP, amyloid precursor protein
- Albumin
- Alzheimer's disease
- Amyloid
- Aß, Amyloid-ß peptide
- CD, Circular dichroism
- CSF, cerebrospinal fluid
- CTerm, albumin C-terminus
- Docking
- HPLC, high performance liquid chromatography
- LC-MS, Liquid chromatography-mass spectrometry
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- NMR, nuclear magnetic resonance
- PBS, phosphate-buffered saline
- PDB, Protein Data Bank
- PPI, protein-protein interactions
- SDS, sodium dodecyl sulfate
- TEM, transmission electron microscopy
- TFA, trifluoroacetic acid
- UV, ultraviolet
- fAβ1–42, HiLyte Fluor488 labelled human Aβ1–42
- β-Sheet
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Affiliation(s)
- Pol Picón-Pagès
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bonet
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier García-García
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Garcia-Buendia
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniela Gutierrez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Valle
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carmen E.S. Gómez-Casuso
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valeriya Sidelkivska
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandra Alvarez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Perálvarez-Marín
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Albert Suades
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - David Andreu
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldomero Oliva
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco J. Muñoz
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Teplyakov A, Obmolova G, Gilliland GL. Structural insights into chemokine CCL17 recognition by antibody M116. Biochem Biophys Rep 2017; 13:27-31. [PMID: 29264403 PMCID: PMC5726885 DOI: 10.1016/j.bbrep.2017.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/21/2022] Open
Abstract
The homeostatic chemokine CCL17, also known as thymus and activation regulated chemokine (TARC), has been associated with various diseases such as asthma, idiopathic pulmonary fibrosis, atopic dermatitis and ulcerative colitis. Neutralization of CCL17 by antibody treatment ameliorates the impact of disease by blocking influx of T cells. Monoclonal antibody M116 derived from a combinatorial library shows potency in neutralizing CCL17-induced signaling. To gain insight into the structural determinants of antigen recognition, the crystal structure of M116 Fab was determined in complex with CCL17 and in the unbound form. Comparison of the structures revealed an unusual induced-fit mechanism of antigen recognition that involves cis-trans isomerization in two CDRs. The structure of the CCL17-M116 complex revealed the antibody binding epitope, which does not overlap with the putative receptor epitope, suggesting that the current model of chemokine-receptor interactions, as observed in the CXCR4-vMIP-II system, may not be universal.
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Key Words
- Antibody
- CCL17
- CDR, complementarity determining region
- Cis-trans isomerization
- Crystal structure
- DTT, dithiothreitol
- EDTA, ethylenediaminetetraacetic acid
- Epitope
- HEPES, 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
- Neutralization
- PDB, Protein Data Bank
- PEG, polyethylene glycol
- RMSD, root-mean-square deviation
- VH, variable domain of the heavy chain
- VL, variable domain of the light chain
- mAb, monoclonal antibody
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Affiliation(s)
- Alexey Teplyakov
- Janssen Research and Development, LLC, Spring House, PA 19477, USA
| | - Galina Obmolova
- Janssen Research and Development, LLC, Spring House, PA 19477, USA
| | - Gary L Gilliland
- Janssen Research and Development, LLC, Spring House, PA 19477, USA
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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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Klarenbeek A, El Mazouari K, Desmyter A, Blanchetot C, Hultberg A, de Jonge N, Roovers RC, Cambillau C, Spinelli S, Del-Favero J, Verrips T, de Haard HJ, Achour I. Camelid Ig V genes reveal significant human homology not seen in therapeutic target genes, providing for a powerful therapeutic antibody platform. MAbs 2016; 7:693-706. [PMID: 26018625 DOI: 10.1080/19420862.2015.1046648] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 01/06/2023] Open
Abstract
Camelid immunoglobulin variable (IGV) regions were found homologous to their human counterparts; however, the germline V repertoires of camelid heavy and light chains are still incomplete and their therapeutic potential is only beginning to be appreciated. We therefore leveraged the publicly available HTG and WGS databases of Lama pacos and Camelus ferus to retrieve the germline repertoire of V genes using human IGV genes as reference. In addition, we amplified IGKV and IGLV genes to uncover the V germline repertoire of Lama glama and sequenced BAC clones covering part of the Lama pacos IGK and IGL loci. Our in silico analysis showed that camelid counterparts of all human IGKV and IGLV families and most IGHV families could be identified, based on canonical structure and sequence homology. Interestingly, this sequence homology seemed largely restricted to the Ig V genes and was far less apparent in other genes: 6 therapeutically relevant target genes differed significantly from their human orthologs. This contributed to efficient immunization of llamas with the human proteins CD70, MET, interleukin (IL)-1β and IL-6, resulting in large panels of functional antibodies. The in silico predicted human-homologous canonical folds of camelid-derived antibodies were confirmed by X-ray crystallography solving the structure of 2 selected camelid anti-CD70 and anti-MET antibodies. These antibodies showed identical fold combinations as found in the corresponding human germline V families, yielding binding site structures closely similar to those occurring in human antibodies. In conclusion, our results indicate that active immunization of camelids can be a powerful therapeutic antibody platform.
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Key Words
- BLAST, basic local alignment search tools
- CDR
- CDR, complementarity-determining region
- FR
- FR, framework region
- HTG, High-Throughput Genomic database
- IGHV, immunoglobulin heavy chain variable region gene
- IGKV, immunoglobulin light chain kappa variable region gene
- IGLV, immunoglobulin light chain lambda variable region gene
- IgG
- PDB, Protein Data Bank
- V family/genes, variable region family/genes
- VH, light chain variable region
- Vκ, light chain kappa variable region
- Vλ, light chain lambda variable region
- WGS, Whole Genome Shotgun database
- antibodies
- biologics
- camelid
- canonical folds
- germline variable genes
- human sequence and structural homology
- sequence mining
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Affiliation(s)
- Alex Klarenbeek
- a Department of Cell Biology; Utrecht University ; Utrecht , The Netherlands
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Casaz P, Boucher E, Wollacott R, Pierce BG, Rivera R, Sedic M, Ozturk S, Thomas WD, Wang Y. Resolving self-association of a therapeutic antibody by formulation optimization and molecular approaches. MAbs 2015; 6:1533-9. [PMID: 25484044 DOI: 10.4161/19420862.2014.975658] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A common challenge encountered during development of high concentration monoclonal antibody formulations is preventing self-association. Depending on the antibody and its formulation, self-association can be seen as aggregation, precipitation, opalescence or phase separation. Here we report on an unusual manifestation of self-association, formation of a semi-solid gel or "gelation." Therapeutic monoclonal antibody C4 was isolated from human B cells based on its strong potency in neutralizing bacterial toxin in animal models. The purified antibody possessed the unusual property of forming a firm, opaque white gel when it was formulated at concentrations >30 mg/mL and the temperature was <6°C. Gel formation was reversible with temperature. Gelation was affected by salt concentration or pH, suggesting an electrostatic interaction between IgG monomers. A comparison of the C4 amino acid sequences to consensus germline sequences revealed differences in framework regions. A C4 variant in which the framework sequence was restored to the consensus germline sequence did not gel at 100 mg/mL at temperatures as low as 1°C. Additional genetic analysis was used to predict the key residue(s) involved in the gelation. Strikingly, a single substitution in the native antibody, replacing heavy chain glutamate 23 with lysine (E23K), was sufficient to prevent gelation. These results indicate that the framework region is involved in intermolecular interactions. The temperature dependence of gelation may be related to conformational changes near glutamate 23 or the regions it interacts with. Molecular engineering of the framework can be an effective approach to resolve the solubility issues of therapeutic antibodies.
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Affiliation(s)
- Paul Casaz
- a MassBiologics of the University of Massachusetts Medical School ; Boston , MA USA
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28
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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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Satoh M, Saburi H, Tanaka T, Matsuura Y, Naitow H, Shimozono R, Yamamoto N, Inoue H, Nakamura N, Yoshizawa Y, Aoki T, Tanimura R, Kunishima N. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation. FEBS Open Bio 2015. [PMID: 26199865 PMCID: PMC4506958 DOI: 10.1016/j.fob.2015.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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] [Indexed: 12/22/2022] Open
Abstract
Keap1 is useful target for the design of drugs that regulate the response to oxidative stresses. We determined two complex crystal structures of Keap1 with a small molecule ligand. The ligand binds to Keap1 so as to mimic the physiological substrate Nrf2. From molecular dynamics simulation results, the binding modes observed may be atypical in solution. Key residues for ligand binding are common between crystal and MD structures.
Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development.
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Affiliation(s)
- Mikiya Satoh
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Hajime Saburi
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Tomoyuki Tanaka
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rieko Shimozono
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Naoyoshi Yamamoto
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Hideki Inoue
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Noriko Nakamura
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Yoshitaka Yoshizawa
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Takumi Aoki
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Ryuji Tanimura
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 10-1, Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan
| | - Naoki Kunishima
- Bio-Specimen Platform Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Corresponding author. Tel.: +81 791 58 2937; fax: +81 791 58 2917.
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Tüdős E, Mészáros B, Fiser A, Simon I. A word of caution about biological inference - Revisiting cysteine covalent state predictions. FEBS Open Bio 2014; 4:310-4. [PMID: 24918043 DOI: 10.1016/j.fob.2014.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/25/2013] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 11/20/2022] Open
Abstract
High prediction accuracy is often believed to validate implicit biological assumptions. Cys redox state predictions assume a local sequence environmental effect. Removing local sequence signals did not reduce prediction accuracy. Cys redox state predictions apparently correlate with subcellular localization. Subcellular localization depends on global sequence composition.
The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools.
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Dorosh L, Rajagopalan N, Loewen MC, Stepanova M. Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants. FEBS Open Bio 2014; 4:496-509. [PMID: 24944884 PMCID: PMC4060014 DOI: 10.1016/j.fob.2014.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 03/21/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 01/29/2023] Open
Abstract
Pyrabactin receptors (PYR) play a central role in abscisic acid (ABA) signal transduction; they are ABA receptors that inhibit type 2C protein phosphatases (PP2C). Molecular aspects contributing to increased basal activity of PYR against PP2C are studied by molecular dynamics (MD) simulations. An extensive series of MD simulations of the apo-form of mutagenized PYR1 as a homodimer and in complex with homology to ABA-insensitive 1 (HAB1) phosphatase are reported. In order to investigate the detailed molecular mechanisms mediating PYR1 activity, the MD data was analyzed by essential collective dynamics (ECD), a novel approach that allows the identification, with atomic resolution, of persistent dynamic correlations based on relatively short MD trajectories. Employing the ECD method, the effects of select mutations on the structure and dynamics of the PYR1 complexes were investigated and considered in the context of experimentally determined constitutive activities against HAB1. Approaches to rationally design constitutively active PYR1 constructs to increase PP2C inhibition are discussed.
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Key Words
- ABA, A8S abscisic acid
- Abscisic acid signaling
- CA, constitutively active
- Constitutively active mutations
- ECD, essential collective dynamics
- Essential collective dynamics analysis
- HAB1, homology to ABA insensitive 1
- MD, molecular dynamics
- Molecular dynamics simulations
- P2M, N-(pyridin-2-ylmethyl) naphthalene-1-sulfonamide or C16H14N2O2S
- PCA, principal component analysis
- PDB, Protein Data Bank
- PP2C, phosphatase type 2C
- PYL, PYR1-like
- PYR1, pyrabactin resistance 1
- PYV, pyrabactin or C16H13BrN2O2S
- Pyrabactin resistance
- RCAR, regulatory component of ABA response
- WT, wild type
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Affiliation(s)
- Lyudmyla Dorosh
- National Research Council of Canada, Edmonton, Alberta, Canada ; Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | | | - Michele C Loewen
- National Research Council of Canada, Saskatoon, Saskatchewan, Canada ; Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Maria Stepanova
- National Research Council of Canada, Edmonton, Alberta, Canada ; Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
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Khara P, Roy M, Chakraborty J, Ghosal D, Dutta TK. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB. FEBS Open Bio 2014; 4:290-300. [PMID: 24918041 PMCID: PMC4048848 DOI: 10.1016/j.fob.2014.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 02/20/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 11/27/2022] Open
Abstract
Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads.
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Affiliation(s)
| | | | | | | | - Tapan K. Dutta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata 700054, India
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Hassan N, Tan TC, Spadiut O, Pisanelli I, Fusco L, Haltrich D, Peterbauer CK, Divne C. Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly. FEBS Open Bio 2013; 3:496-504. [PMID: 24282677 PMCID: PMC3839853 DOI: 10.1016/j.fob.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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: 10/28/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/17/2022] Open
Abstract
The flavin-dependent homotetrameric enzyme pyranose 2-oxidase (P2O) is found mostly, but not exclusively, in lignocellulose-degrading fungi where it catalyzes the oxidation of β-d-glucose to the corresponding 2-keto sugar concomitantly with hydrogen peroxide formation during lignin solubilization. Here, we present crystal structures of P2O from the efficient lignocellulolytic basidiomycete Phanerochaete chrysosporium. Structures were determined of wild-type PcP2O from the natural fungal source, and two variants of recombinant full-length PcP2O, both in complex with the slow substrate 3-deoxy-3-fluoro-β-d-glucose. The active sites in PcP2O and P2O from Trametes multicolor (TmP2O) are highly conserved with identical substrate binding. Our structural analysis suggests that the 17 °C higher melting temperature of PcP2O compared to TmP2O is due to an increased number of intersubunit salt bridges. The structure of recombinant PcP2O expressed with its natural N-terminal sequence, including a proposed propeptide segment, reveals that the first five residues of the propeptide intercalate at the interface between A and B subunits to form stabilizing, mainly hydrophobic, interactions. In the structure of mature PcP2O purified from the natural source, the propeptide segment in subunit A has been replaced by a nearby loop in the B subunit. We propose that the propeptide in subunit A stabilizes the A/B interface of essential dimers in the homotetramer and that, upon maturation, it is replaced by the loop in the B subunit to form the mature subunit interface. This would imply that the propeptide segment of PcP2O acts as an intramolecular chaperone for oligomerization at the A/B interface of the essential dimer. Structures of pyranose 2-oxidase from Phanerochaete chrysosporium were determined. The N-terminus may act as a propeptide with a role in homotetramer assembly. A large number of salt bridges between subunits provides thermostability. The substrate is bound in the productive binding mode for oxidation at C2.
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Key Words
- 2FGlc, 2-deoxy-2-fluoro-d-glucose
- 3FGlc, 3-deoxy-3-fluoro-d-glucose
- Crystal structure
- DTT, dithiothreitol
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- IMAC, by immobilized metal ion affinity chromatography
- IPTG, β-d-1-thiogalactopyranoside
- Lignin degradation
- MES, 2-(N-morpholino) ethanesulfonic acid
- MWCO, molecular weight cut off
- Oligomerization
- P2O, pyranose oxidase
- PBS, phosphate buffered saline
- PDB, Protein Data Bank
- PEG, polyethylene glycol
- Propeptide
- Pyranose 2-oxidase
- TEV, Tobacco Etch Virus
- Thermostability
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Affiliation(s)
- Noor Hassan
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Tien-Chye Tan
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
| | - Oliver Spadiut
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Ines Pisanelli
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Laura Fusco
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Dietmar Haltrich
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Clemens K. Peterbauer
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Christina Divne
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
- Corresponding author at: KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691StockholmSweden. Tel.: +46 8 55378296; fax: +46 8 55378468.
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Faggiano S, Menon RP, Kelly GP, McCormick J, Todi SV, Scaglione KM, Paulson HL, Pastore A. Enzymatic production of mono-ubiquitinated proteins for structural studies: The example of the Josephin domain of ataxin-3. FEBS Open Bio 2013; 3:453-8. [PMID: 24251111 PMCID: PMC3829987 DOI: 10.1016/j.fob.2013.10.005] [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: 08/30/2013] [Revised: 10/07/2013] [Accepted: 10/07/2013] [Indexed: 12/03/2022] Open
Abstract
Protein ubiquitination occurs through formation of an isopeptide bond between the C-terminal glycine of ubiquitin (Ub) and the ɛ-amino group of a substrate lysine residue. This post-translational modification, which occurs through the attachment of single and/or multiple copies of mono-ubiquitin and poly-ubiquitin chains, is involved in crucial cellular events such as protein degradation, cell-cycle regulation and DNA repair. The abnormal functioning of ubiquitin pathways is also implicated in the pathogenesis of several human diseases ranging from cancer to neurodegeneration. However, despite the undoubted biological importance, understanding the molecular basis of how ubiquitination regulates different pathways has up to now been strongly limited by the difficulty of producing the amounts of highly homogeneous samples that are needed for a structural characterization by X-ray crystallography and/or NMR. Here, we report on the production of milligrams of highly pure Josephin mono-ubiquitinated on lysine 117 through large scale in vitro enzymatic ubiquitination. Josephin is the catalytic domain of ataxin-3, a protein responsible for spinocerebellar ataxia type 3. Ataxin-3 is the first deubiquitinating enzyme (DUB) reported to be activated by mono-ubiquitination. We demonstrate that the samples produced with the described method are correctly folded and suitable for structural studies. The protocol allows facile selective labelling of the components. Our results provide an important proof-of-concept that may pave the way to new approaches to the in vitro study of ubiquitinated proteins. We set up a protocol for large-scale in vitro enzymatic ubiqitination. This produced milligrams of highly pure mono-ubiquitinated Josephin domain of ataxin-3. We applied an alternative labelling scheme for the structural characterization of the sample by NMR. Ubiquitin covalently linked on lysine 117 directly interacts with Josephin but does not alter the overall fold of the protein.
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Key Words
- ATP, adenosine triphosphate
- DTT, dithiothreitol
- DUB, deubiquitinating enzyme
- Deubiquitinating enzyme
- GST, glutathione-S-transferase
- HSQC, heteronuclear single quantum coherence
- IAA, iodoacetamide
- Isopeptide bond
- JosK117-only, Josephin mutant in which all lysines but K117 are mutated
- Josephin
- MS/MS tandem, mass spectrometry
- Machado–Joseph disease
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Post-translational modification
- SDS–PAGE, sodium dodecyl sulfate–polyacrylamide gel electrophoresis
- Spinocerebellar ataxia type 3
- Tris–HCl, 2-amino-2-(hydroxymethyl)-1,3-propanediol hydrochloride
- Ubiquitin
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Affiliation(s)
- Serena Faggiano
- National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
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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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Lee SJ, Seo E, Cho Y. Proposal for a new therapy for drug-resistant malaria using Plasmodium synthetic lethality inference. Int J Parasitol Drugs Drug Resist 2013; 3:119-28. [PMID: 24533301 PMCID: PMC3862410 DOI: 10.1016/j.ijpddr.2013.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 01/01/2013] [Revised: 06/02/2013] [Accepted: 06/05/2013] [Indexed: 01/18/2023]
Abstract
Many antimalarial drugs kill malaria parasites, but antimalarial drug resistance (ADR) and toxicity to normal cells limit their usefulness. To solve this problem, we suggest a new therapy for drug-resistant malaria. The approach consists of data integration and inference through homology analysis of yeast-human-Plasmodium. If one gene of a Plasmodium synthetic lethal (SL) gene pair has a mutation that causes ADR, a drug targeting the other gene of the SL pair might be used as an effective treatment for drug-resistant strains of malaria. A simple computational tool to analyze the inferred SL genes of Plasmodium species (malaria parasites Plasmodium falciparum and Plasmodium vivax for human malarial therapy, and rodent parasite Plasmodium berghei for in vivo studies of human malarias) was established to identify SL genes that can be used as drug targets. Information on SL gene pairs with ADR genes and their first neighbors was inferred from yeast SL genes to search for pertinent antimalarial drug targets. We not only suggest drug target gene candidates for further experimental validation, but also provide information on new usage for already-described drugs. The proposed specific antimalarial drug candidates can be inferred by searching drugs that cause a fitness defect in yeast SL genes.
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Affiliation(s)
- Sang Joon Lee
- Center for Biofluid and Biomimic Research, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), San 31, Hyoja Dong, Namgu, Pohang 790-784, Republic of Korea
| | - Eunseok Seo
- Center for Biofluid and Biomimic Research, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), San 31, Hyoja Dong, Namgu, Pohang 790-784, Republic of Korea
| | - Yonghyun Cho
- Samsumg SDS, Trade Center ASEM Tower, Samseong 1-dong, Gangnam-gu, Seoul 135-798, Republic of Korea
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Hischenhuber B, Frommlet F, Schreiner W, Knapp B. MH 2c: Characterization of major histocompatibility α-helices - an information criterion approach. Comput Phys Commun 2012; 183:1481-1490. [PMID: 23564964 PMCID: PMC3617674 DOI: 10.1016/j.cpc.2012.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/20/2012] [Accepted: 02/02/2012] [Indexed: 06/02/2023]
Abstract
UNLABELLED Major histocompatibility proteins share a common overall structure or peptide binding groove. Two binding groove domains, on the same chain for major histocompatibility class I or on two different chains for major histocompatibility class II, contribute to that structure that consists of two α-helices ("wall") and a sheet of eight anti-parallel beta strands ("floor"). Apart from the peptide presented in the groove, the major histocompatibility α-helices play a central role for the interaction with the T cell receptor. This study presents a generalized mathematical approach for the characterization of these helices. We employed polynomials of degree 1 to 7 and splines with 1 to 2 nodes based on polynomials of degree 1 to 7 on the α-helices projected on their principal components. We evaluated all models with a corrected Akaike Information Criterion to determine which model represents the α-helices in the best way without overfitting the data. This method is applicable for both the stationary and the dynamic characterization of α-helices. By deriving differential geometric parameters from these models one obtains a reliable method to characterize and compare α-helices for a broad range of applications. PROGRAM SUMMARY Program title: MH2c (MH helix curves) Catalogue identifier: AELX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 327 565 No. of bytes in distributed program, including test data, etc.: 17 433 656 Distribution format: tar.gz Programming language: Matlab Computer: Personal computer architectures Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed) RAM: Depends on the trajectory size, min. 1 GB (Matlab) Classification: 2.1, 4.9, 4.14 External routines: Curve Fitting Toolbox and Statistic Toolbox of Matlab Nature of problem: Major histocompatibility (MH) proteins share a similar overall structure. However, identical MH alleles which present different peptides differ by subtle conformational alterations. One hypothesis is that such conformational differences could be another level of T cell regulation. By this software package we present a reliable and systematic way to compare different MH structures to each other. Solution method: We tested several fitting approaches on all available experimental crystal structures of MH to obtain an overall picture of how to describe MH helices. For this purpose we transformed all complexes into the same space and applied splines and polynomials of several degrees to them. To draw a general conclusion which method fits them best we employed the "corrected Akaike Information Criterion". The software is applicable for all kinds of helices of biomolecules. Running time: Depends on the data, for a single stationary structure the runtime should not exceed a few seconds.
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Key Words
- AIC, Akaike Information Criterion
- Akaike Information Criterion
- CDR, complementarity determining region
- Conformational changes
- G, binding groove
- Helix
- IMGT®, the international ImMunoGeneTics information system®
- MD, Molecular Dynamics
- MH
- MH, major histocompatibility
- MH1, major histocompatibility class I
- MH2, major histocompatibility class II
- MH2c, MH helix curves (name of software)
- MHC
- Minimization and fitting
- Molecular dynamics simulation
- PC, principal component
- PCA, Principal Component Analysis
- PDB, Protein Data Bank
- Proteins
- Secondary structure
- Structure and properties
- TR, T cell receptor
- Theory, modeling, and computer simulation
- Utility
- VMD, Visual Molecular Dynamics
- cAIC, corrected Akaike Information Criterion
- p, peptide
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Affiliation(s)
- B. Hischenhuber
- Center for Medical Statistics, Informatics, and Intelligent Systems; Section for Biosimulation and Bioinformatics, Medical University of Vienna, Austria
| | - F. Frommlet
- Center for Medical Statistics, Informatics, and Intelligent Systems; Section for Medical Statistics, Medical University of Vienna, Austria
| | - W. Schreiner
- Center for Medical Statistics, Informatics, and Intelligent Systems; Section for Biosimulation and Bioinformatics, Medical University of Vienna, Austria
| | - B. Knapp
- Center for Medical Statistics, Informatics, and Intelligent Systems; Section for Biosimulation and Bioinformatics, Medical University of Vienna, Austria
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Abstract
Cysteine has been considered as a “hydrophilic” amino acid because of its pKa and its ability to form (weak) hydrogen bonds. However, cysteines are found mostly in hydrophobic environments, either in S–S (disulphide) form or in free cysteine form. When free cysteines are found on the surface of proteins, they are often involved in catalytic residues, as in cysteine proteases, P-loop phosphatases, etc. Additionally, a unique property of cysteines is that their side-chain volume is different from all other amino acids. This study is focused on the discrimination between structural versus active free cysteines based on a local environment analysis which does not appear to have been attempted previously. We have demonstrated the corresponding structural positions associated with free cysteines in their three-dimensional localization environment. We examined protein samples including nine, sequenced, coronavirus proteases and cysteine-rich non-membrane proteins. Our present study shows that the sequential environments of free cysteines of coronavirus proteases are rather hydrophobic and that the free cysteines of non-membrane proteases have a higher amount of contacts to hydrophobic residues and lower amount of contacts to polar or charged residues.
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Key Words
- C, cysteine
- Free cysteine
- HSSP, a database of homology-derived secondary structure of proteins
- Hydrophobic
- PDB, Protein Data Bank
- PERL, Practical Extraction and Report Language, a dynamic programming language
- Proteases
- RMSD, the square deviations
- SH
- SH, free cysteine form
- SS
- SS, disulphide from
- Spatial neighborhood
- Structural bioinformatics
- Structural preference
- aa, amino acid
- pro, main proteinase
- Å, RMSD from the crystal structure of the complex
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Affiliation(s)
- Sheau Ling Ho
- Department of Chemical Engineering, Chinese Culture University, Taipei 111, Taiwan
- Corresponding author.
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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