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Lorrine OE, Rahman RNZRA, Joo Shun T, Salleh AB, Oslan SN. In silico structural exploration of serine protease from a CTG-clade yeast Meyerozyma guilliermondii strain SO. Anal Biochem 2023; 668:115092. [PMID: 36889624 DOI: 10.1016/j.ab.2023.115092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
In eukaryotes, serine proteases are cellular localized hydrolases reported to regulate essential biological reactions. Improved industrial applications of proteins are aided by prediction and analysis of their 3-dimensional structures (3D). A serine protease was identified from CTG-clade yeast Meyerozyma guilliermondii strain SO and its 3D structure as well as its catalytic attributes have not been fully understood yet, thus we seek to report on the catalytic mechanism of M. guilliermondii strain SO MgPRB1 using substrate PMSF via in silico docking as well as its stability by way of disulfide bonds formation. Herein, bioinformatics tools and techniques were used to predict, validate and analyze the possible changes of CUG ambiguity (if any) in strain SO using template PDB ID: 3F7O. Structural assessments confirmed the classic catalytic triad Asp305, His337, and Ser499. Superimposition of MgPRB1 and template 3F7O structures revealed the unlinked cysteine residues between Cys341, Cys440, Cys471 and Cys506 of MgPRB1 compared to template 3F7O with two disulfide bonds formation, which confers structural stability. In conclusion, serine protease structure from strain SO was successfully predicted and studies towards understanding at the molecular level may be undertaken for its potential applications in the degradation of peptide bonds.
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Affiliation(s)
- Okojie Eseoghene Lorrine
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Tan Joo Shun
- School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Homology Modeling and Analysis of Vacuolar Aspartyl Protease from a Novel Yeast Expression Host Meyerozyma guilliermondii Strain SO. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-07153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Rantam FA, Kharisma VD, Sumartono C, Nugraha J, Wijaya AY, Susilowati H, Kuncorojakti S, Nugraha AP. Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach. F1000Res 2021; 10. [PMID: 34909175 PMCID: PMC8596179 DOI: 10.12688/f1000research.54258.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/20/2022] Open
Abstract
Background: An immunoinformatic approach may be useful to investigate the conserved region in the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting the conserved regions in the spike glycoprotein to trigger increased multi-variant virus neutralization and memory response for the development of vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia were compared with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates obtained from the NCBI and GISAID databases. The recognition of antigens was carried out directly using B cells through the B cell receptor (BCR). An indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC 50 value. In addition, vaccine allergenicity and toxicity were investigated. During the molecular complex examination, the 3D peptide structure was investigated and the lowest amount of energy formed when the vaccine candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved regions which were very similar to reference countries such as China, the United Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was predicted that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidate with antigenic, non-allergen, and non-toxic properties.
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Affiliation(s)
- Fedik Abdul Rantam
- Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia.,Virology and Immunology Laboratory, Department of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia
| | - Viol Dhea Kharisma
- Biology Department, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, East Java, Indonesia
| | - Christrijogo Sumartono
- Anasthesiology and Reanimation Department, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga,, Surabaya, East Java, Indonesia
| | - Jusak Nugraha
- Clinical Pathology Department,, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Andi Yasmin Wijaya
- Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Helen Susilowati
- Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Suryo Kuncorojakti
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
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Structure Prediction of a Thermostable SR74 α-Amylase from Geobacillus stearothermophilus Expressed in CTG-Clade Yeast Meyerozyma guilliermondii Strain SO. Catalysts 2020. [DOI: 10.3390/catal10091059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
α-amylase which catalyzes the hydrolysis of α-1,4-glycosidic bonds in starch have frequently been cloned into various microbial workhorses to yield a higher recombinant titer. A thermostable SR74 α-amylase from Geobacillus stearothermophilus was found to have a huge potential in detergent industries due to its thermostability properties. The gene was cloned into a CTG-clade yeast Meyerozyma guilliermondii strain SO. However, the CUG ambiguity present in the strain SO has possibly altered the amino acid residues in SR74 amylase wild type (WT) encoded by CUG the codon from the leucine to serine. From the multiple sequence alignment, six mutations were found in recombinant SR74 α-amylase (rc). Their effects on SR74 α-amylase structure and function remain unknown. Herein, we predicted the structures of the SR74 amylases (WT and rc) using the template 6ag0.1.A (PDB ID: 6ag0). We sought to decipher the possible effects of CUG ambiguity in strain SO via in silico analysis. They are structurally identical, and the metal triad (CaI–CaIII) might contribute to the thermostability while CaIV was attributed to substrate specificity. Since the pairwise root mean square deviation (RMSD) between the WT and rc SR74 α-amylase was lower than the template, we suggest that the biochemical properties of rc SR74 α-amylase were better deduced from its WT, especially its thermostability.
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Papadopoulou LC, Ingendoh-Tsakmakidis A, Mpoutoureli CN, Tzikalou LD, Spyridou ED, Gavriilidis GI, Kaiafas GC, Ntaska AT, Vlachaki E, Panayotou G, Samiotaki M, Tsiftsoglou AS. Production and Transduction of a Human Recombinant β-Globin Chain into Proerythroid K-562 Cells To Replace Missing Endogenous β-Globin. Mol Pharm 2018; 15:5665-5677. [PMID: 30375878 DOI: 10.1021/acs.molpharmaceut.8b00857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein replacement therapy (PRT) has been applied to treat severe monogenetic/metabolic disorders characterized by a protein deficiency. In disorders where an intracellular protein is missing, PRT is not easily feasible due to the inability of proteins to cross the cell membrane. Instead, gene therapy has been applied, although still with limited success. β-Thalassemias are severe congenital hemoglobinopathies, characterized by deficiency or reduced production of the adult β-globin chain. The resulting imbalance of α-/β-globin chains of adult hemoglobin (α2β2) leads to precipitation of unpaired α-globin chains and, eventually, to defective erythropoiesis. Since protein transduction domain (PTD) technology has emerged as a promising therapeutic approach, we produced a human recombinant β-globin chain in fusion with the TAT peptide and successfully transduced it into human proerythroid K-562 cells, deficient in mature β-globin chain. Notably, the produced human recombinant β-globin chain without the TAT peptide, used as internal negative control, failed to be transduced into K-562 cells under similar conditions. In silico studies complemented by SDS-PAGE, Western blotting, co-immunoprecipitation and LC-MS/MS analysis indicated that the transduced recombinant fusion TAT-β-globin protein interacts with the endogenous native α-like globins to form hemoglobin α2β2-like tetramers to a limited extent. Our findings provide evidence that recombinant TAT-β-globin is transmissible into proerythroid K-562 cells and can be potentially considered as an alternative protein therapeutic approach for β-thalassemias.
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Affiliation(s)
- Lefkothea C Papadopoulou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Alexandra Ingendoh-Tsakmakidis
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Christina N Mpoutoureli
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Lamprini D Tzikalou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Efthymia D Spyridou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - George I Gavriilidis
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Georgios C Kaiafas
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Agoritsa T Ntaska
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
| | - Efthymia Vlachaki
- Adult Thalassemia Unit , Hippokrateion General Hospital , Thessaloniki 54642 , Greece
| | | | | | - Asterios S Tsiftsoglou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences , Aristotle University of Thessaloniki , Thessaloniki 54124 , Macedonia , Greece
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Kumar V, Sonani RR, Sharma M, Gupta GD, Madamwar D. Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM. PHOTOSYNTHESIS RESEARCH 2016; 129:17-28. [PMID: 27068646 DOI: 10.1007/s11120-016-0259-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/31/2016] [Indexed: 05/22/2023]
Abstract
The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the β-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and β- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of β-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.
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Affiliation(s)
- Vinay Kumar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - Ravi R Sonani
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No-39, Vallabh Vidyanagar, 388120, India
| | - Mahima Sharma
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Gagan D Gupta
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No-39, Vallabh Vidyanagar, 388120, India.
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7
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Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G, Coll M. Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Sci Rep 2016; 6:20915. [PMID: 26875695 PMCID: PMC4753449 DOI: 10.1038/srep20915] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/13/2016] [Indexed: 11/16/2022] Open
Abstract
DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - José Angel Ruiz-Masó
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Manuel Rueda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Departament de Bioquímica, Facultat de Biologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Gloria del Solar
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
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8
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Balaji S. Internal symmetry in protein structures: prevalence, functional relevance and evolution. Curr Opin Struct Biol 2015; 32:156-66. [PMID: 26093245 DOI: 10.1016/j.sbi.2015.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Abstract
Symmetry has been found at various levels of biological organization in the protein structural universe. Numerous evolutionary studies have proposed connections between internal symmetry within protein tertiary structures, quaternary associations and protein functions. Recent computational methods, such as SymD and CE-Symm, facilitate a large-scale detection of internal symmetry in protein structures. Based on the results from these methods, about 20% of SCOP folds, superfamilies and families are estimated to have structures with internal symmetry (Figure 1d). All-β and membrane proteins fold classes contain a relatively high number of unique instances of internal symmetry. In addition to the axis of symmetry, anecdotal evidence suggests that, the region of connection or contact between symmetric units could coincide with functionally relevant sites within a fold. General principles that underlie protein internal symmetry and their connections to protein structural integrity and functions remain to be elucidated.
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Affiliation(s)
- Santhanam Balaji
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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