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Chauhan R, Nate Z, Ike B, Kwabena Adu D, Alake J, Gill AAS, Miya L, Bachheti Thapliyal N, Karpoormath R. One pot fabrication of diamino naphthalene -AuNPs decorated graphene nanoplatform for the MRSA detection in the biological sample. Bioelectrochemistry 2024; 157:108674. [PMID: 38460467 DOI: 10.1016/j.bioelechem.2024.108674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/11/2024]
Abstract
Early monitoring of MRSA can effectively mitigate the disease risk by using Penicillin-binding protein 2a (PbP2a) biomarker. Diamino naphthalene-AuNPs decorated graphene (AuNPsGO-DN) nanocomposite was synthesized for a rapid and sensitive immunosensor detecting PbP2a. The synthesized AuNPsGO-DN nanocomposites were characterized by field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (SEM-EDX), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, and X-ray diffraction spectroscopy (XRD). Electrochemical characterization done with cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrical impedance spectroscopy (EIS) techniques. Anti-PbP2a monoclonal antibodies immobilized at AuNPsGO-DN/GCE via covalent bonding. AuNPs enhanced the electrode surface area and the antibodies' loading. Mercaptopropionic acid (MPA) was a linker between the AuNPs and antibodies, orientated the antibodies as opposite to the PbP2a antigen, and improved the sensitivity and specificity. The antiPbP2a/MPA/AuNPsGO-DN/GCE electrode displayed sensitive and selective detection towards the PbP2a antigen in phosphate buffer saline (PBS pH 7.4). The broad linear range from 0.01 to 8000 pg/mL was obtained with LOD of 0.154 pg/mL and 0.0239 pg/mL, respectively. A label-free, simple, and sensitive immunosensor was developed with a 98-106 % recovery rate in spiked biological samples. It shows the potential applicability of the developed immunoelectrode.
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Affiliation(s)
- Ruchika Chauhan
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Zondi Nate
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Blessing Ike
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Darko Kwabena Adu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - John Alake
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Atal A S Gill
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Lungelo Miya
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Neeta Bachheti Thapliyal
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa.
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2
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Chang YC, Cao Z, Chen WT, Huang WC. Effects of stand-alone polar residue on membrane protein stability and structure. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184325. [PMID: 38653423 DOI: 10.1016/j.bbamem.2024.184325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Helical membrane proteins generally have a hydrophobic nature, with apolar side chains comprising the majority of the transmembrane (TM) helices. However, whenever polar side chains are present in the TM domain, they often exert a crucial role in structural interactions with other polar residues, such as TM helix associations and oligomerization. Moreover, polar residues in the TM region also often participate in protein functions, such as the Schiff base bonding between Lys residues and retinal in rhodopsin-like membrane proteins. Although many studies have focused on these functional polar residues, our understanding of stand-alone polar residues that are energetically unfavored in TM helixes is limited. Here, we adopted bacteriorhodopsin (bR) as a model system and systematically mutated 17 of its apolar Leu or Phe residues to polar Asn. Stability measurements of the resulting mutants revealed that all of these polar substitutions reduced bR stability to various extents, and the extent of destabilization of each mutant bR is also correlated to different structural factors, such as the relative accessible surface area and membrane depth of the mutation site. Structural analyses of these Asn residues revealed that they form sidechain-to-backbone hydrogen bonds that alleviate the unfavorable energetics in hydrophobic and apolar surroundings. Our results indicate that membrane proteins are able to accommodate certain stand-alone polar residues in the TM region without disrupting overall structures.
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Affiliation(s)
- Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Zheng Cao
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, CA 90095, United States of America
| | - Wai-Ting Chen
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chun Huang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
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Vijayanathan M, Vadakkepat AK, Mahendran KR, Sharaf A, Frandsen KEH, Bandyopadhyay D, Pillai MR, Soniya EV. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity. Commun Biol 2024; 7:566. [PMID: 38745065 PMCID: PMC11093982 DOI: 10.1038/s42003-024-06152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS's steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
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Affiliation(s)
- Mallika Vijayanathan
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Abhinav Koyamangalath Vadakkepat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE17HB, UK
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
| | - Kristian E H Frandsen
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Eppurath Vasudevan Soniya
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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Hoda A, Bixheku X, Lika Çekani M. Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR geneComputational analysis of bovine PKLR gene. J Biomol Struct Dyn 2024; 42:4155-4168. [PMID: 37278385 DOI: 10.1080/07391102.2023.2219315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the PKLR gene by using several computational tools. In silico tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins' stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated via Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anila Hoda
- Agricultural University of Tirana, Tirana, Albania
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Siva Sankari G, James R, Payva F, Sivaramakrishnan V, Vineeth Kumar TV, Kanchi S, Santhy KS. Computational analysis of sodium-dependent phosphate transporter SLC20A1/PiT1 gene identifies missense variations C573F, and T58A as high-risk deleterious SNPs. J Biomol Struct Dyn 2024; 42:4072-4086. [PMID: 37286379 DOI: 10.1080/07391102.2023.2218939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
SLC20A1/PiT1 is a sodium-dependent inorganic phosphate transporter, initially recognized as the retroviral receptor for Gibbon Ape Leukemia Virus in humans. SNPs in SLC20A1 is associated with Combined Pituitary Hormone Deficiency and Sodium Lithium Counter transport. Using in silico techniques, we have screened the nsSNPs for their deleterious effect on the structure and function of SLC20A1. Screening with sequence and structure-based tools on 430 nsSNPs, filtered 17 nsSNPs which are deleterious. To evaluate the role of these SNPs, protein modeling and MD simulations were performed. A comparative analysis of model generated with SWISS-MODEL and AlphaFold shows that many residues are in the disallowed region of Ramachandran plot. Since SWISS-MODEL structure has a 25-residue deletion, the AlphaFold structure was used to perform MD simulation for equilibration and structure refinement. Further, to understand perturbation of energetics, we performed in silico mutagenesis and ΔΔG calculation using FoldX on MD refined structures, which yielded SNPs that are neutral (3), destabilizing (12) and stabilizing (2) on protein structure. Furthermore, to elucidate the impact of SNPs on structure, we performed MD simulations to discern the changes in RMSD, Rg, RMSF and LigPlot of interacting residues. RMSF profiles of representative SNPs revealed that A114V (neutral) and T58A (positive) were more flexible & C573F (negative) was more rigid compared to wild type, which is also reflected in the changes in number of local interacting residues in LigPlot and ΔΔG. Taken together, our results show that SNPs can lead to structural perturbations and impact the function of SLC20A1 with potential implications for disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Siva Sankari
- Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala, India
| | - Remya James
- St. Joseph's College for Women, Alappuzha, Kerala, India
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
| | - Febby Payva
- St. Joseph's College for Women, Alappuzha, Kerala, India
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | | | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - K S Santhy
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
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Ayodele AO, Udosen B, Oluwagbemi OO, Oladipo EK, Omotuyi I, Isewon I, Nash O, Soremekun O, Fatumo S. An in-silico analysis of OGT gene association with diabetes mellitus. BMC Res Notes 2024; 17:89. [PMID: 38539217 PMCID: PMC10976716 DOI: 10.1186/s13104-024-06744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
O-GlcNAcylation is a nutrient-sensing post-translational modification process. This cycling process involves two primary proteins: the O-linked N-acetylglucosamine transferase (OGT) catalysing the addition, and the glycoside hydrolase OGA (O-GlcNAcase) catalysing the removal of the O-GlCNAc moiety on nucleocytoplasmic proteins. This process is necessary for various critical cellular functions. The O-linked N-acetylglucosamine transferase (OGT) gene produces the OGT protein. Several studies have shown the overexpression of this protein to have biological implications in metabolic diseases like cancer and diabetes mellitus (DM). This study retrieved 159 SNPs with clinical significance from the SNPs database. We probed the functional effects, stability profile, and evolutionary conservation of these to determine their fit for this research. We then identified 7 SNPs (G103R, N196K, Y228H, R250C, G341V, L367F, and C845S) with predicted deleterious effects across the four tools used (PhD-SNPs, SNPs&Go, PROVEAN, and PolyPhen2). Proceeding with this, we used ROBETTA, a homology modelling tool, to model the proteins with these point mutations and carried out a structural bioinformatics method- molecular docking- using the Glide model of the Schrodinger Maestro suite. We used a previously reported inhibitor of OGT, OSMI-1, as the ligand for these mutated protein models. As a result, very good binding affinities and interactions were observed between this ligand and the active site residues within 4Å of OGT. We conclude that these mutation points may be used for further downstream analysis as drug targets for treating diabetes mellitus.
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Affiliation(s)
- Abigail O Ayodele
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Brenda Udosen
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
| | - Olugbenga O Oluwagbemi
- Department of Computer Science and Information Technology, Faculty of Natural and Applied Sciences, Sol Plaatje University, 8301, Kimberley, South Africa
- Department of Mathematical Sciences, Stellenbosch University, 7602, Stellenbosch, South Africa
| | - Elijah K Oladipo
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, 232104, Ede, Nigeria
- Genomics Unit, Helix Biogen Institute, 210214, Ogbomoso, Nigeria
| | - Idowu Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria
- Molecular Biology and Molecular Simulation Center (Mols&Sims), Ado Ekiti, Nigeria
| | - Itunuoluwa Isewon
- Computer and Information Sciences Department, Covenant University, Ota, Ogun State, Nigeria
| | - Oyekanmi Nash
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
- MRC/UVRI and London School of Hygiene and Tropical Medicine London (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Segun Fatumo
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
- MRC/UVRI and London School of Hygiene and Tropical Medicine London (LSHTM) Uganda Research Unit, Entebbe, Uganda.
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7
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Osterne VJ, Pinto-Junior VR, Oliveira MV, Nascimento KS, Van Damme EJ, Cavada BS. Computational insights into the circular permutation roles on ConA binding and structural stability. Curr Res Struct Biol 2024; 7:100140. [PMID: 38559841 PMCID: PMC10979261 DOI: 10.1016/j.crstbi.2024.100140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
The mechanisms behind Concanavalin A (ConA) circular permutation have been under investigation since 1985. Although a vast amount of information is available about this lectin and its applications, the exact purpose of its processing remains unclear. To shed light on this, this study employed computer simulations to compare the unprocessed ProConA with the mature ConA. This approach aimed to reveal the importance of the post-translational modifications, especially how they affect the lectin stability and carbohydrate-binding properties. To achieve these goals, we conducted 200 ns molecular dynamics simulations and trajectory analyses on the monomeric forms of ProConA and ConA (both unbound and in complex with D-mannose and the GlcNAc2Man9 N-glycan), as well as on their oligomeric forms. Our findings reveal significant stability differences between ProConA and ConA at both the monomeric and tetrameric levels, with ProConA exhibiting consistently lower stability parameters compared to ConA. In terms of carbohydrate binding properties, however, both lectins showed remarkable similarities in their interaction profiles, contact numbers, and binding free energies with D-mannose and the high-mannose N-glycan. Overall, our results suggest that the processing of ProConA significantly enhances the stability of the mature lectin, especially in maintaining the tetrameric oligomer, without substantially affecting its carbohydrate-binding properties.
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Affiliation(s)
- Vinicius J.S. Osterne
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
- Department of Physics, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
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Harihar B, Saravanan KM, Gromiha MM, Selvaraj S. Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design. Mol Biotechnol 2024:10.1007/s12033-024-01119-4. [PMID: 38498284 DOI: 10.1007/s12033-024-01119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein-protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.
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Affiliation(s)
- Balasubramanian Harihar
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
| | - Konda Mani Saravanan
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600073, India
| | - Michael M Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India
| | - Samuel Selvaraj
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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Veríssimo NVP, Mussagy CU, Bento HBS, Pereira JFB, Santos-Ebinuma VDC. Ionic liquids and deep eutectic solvents for the stabilization of biopharmaceuticals: A review. Biotechnol Adv 2024; 71:108316. [PMID: 38199490 DOI: 10.1016/j.biotechadv.2024.108316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Biopharmaceuticals have allowed the control of previously untreatable diseases. However, their low solubility and stability still hinder their application, transport, and storage. Hence, researchers have applied different compounds to preserve and enhance the delivery of biopharmaceuticals, such as ionic liquids (ILs) and deep eutectic solvents (DESs). Although the biopharmaceutical industry can employ various substances for enhancing formulations, their effect will change depending on the properties of the target biomolecule and environmental conditions. Hence, this review organized the current state-of-the-art on the application of ILs and DESs to stabilize biopharmaceuticals, considering the properties of the biomolecules, ILs, and DESs classes, concentration range, types of stability, and effect. We also provided a critical discussion regarding the potential utilization of ILs and DESs in pharmaceutical formulations, considering the restrictions in this field, as well as the advantages and drawbacks of these substances for medical applications. Overall, the most applied IL and DES classes for stabilizing biopharmaceuticals were cholinium-, imidazolium-, and ammonium-based, with cholinium ILs also employed to improve their delivery. Interestingly, dilute and concentrated ILs and DESs solutions presented similar results regarding the stabilization of biopharmaceuticals. With additional investigation, ILs and DESs have the potential to overcome current challenges in biopharmaceutical formulation.
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Affiliation(s)
- Nathalia Vieira Porphirio Veríssimo
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil; Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, São Paulo University, CEP: 14040-020 Ribeirão Preto, SP, Brazil.
| | - Cassamo Usemane Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile.
| | - Heitor Buzetti Simões Bento
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
| | | | - Valéria de Carvalho Santos-Ebinuma
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University, CEP: 14801-902 Araraquara, SP, Brazil.
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Simões R, Ribeiro AC, Dias R, Freitas V, Soares S, Pérez-Gregorio R. Unveiling the Immunomodulatory Potential of Phenolic Compounds in Food Allergies. Nutrients 2024; 16:551. [PMID: 38398875 PMCID: PMC10891931 DOI: 10.3390/nu16040551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Food allergies are becoming ever more prevalent around the world. This pathology is characterized by the breakdown of oral tolerance to ingested food allergens, resulting in allergic reactions in subsequent exposures. Due to the possible severity of the symptoms associated with this pathology, new approaches to prevent it and reduce associated symptoms are of utmost importance. In this framework, dietary phenolic compounds appear as a tool with a not fully explored potential. Some phenolic compounds have been pointed to with the ability to modulate food allergies and possibly reduce their symptoms. These compounds can modulate food allergies through many different mechanisms, such as altering the bioaccessibility and bioavailability of potentially immunogenic peptides, by modulating the human immune system and by modulating the composition of the human microbiome that resides in the oral cavity and the gastrointestinal tract. This review deepens the state-of-the-art of the modulation of these mechanisms by phenolic compounds. While this review shows clear evidence that dietary supplementation with foods rich in phenolic compounds might constitute a new approach to the management of food allergies, it also highlights the need for further research to delve into the mechanisms of action of these compounds and decipher systematic structure/activity relationships.
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Affiliation(s)
- Rodolfo Simões
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
- Food and Health Omics Group, Food and Agroecology Institute, University of Vigo, Campus As Lagoas, s/n, 32004 Ourense, Spain
- Food and Health Omics Group, Department of Chemistry and Biochemistry, Galicia Sur Health Research Institute (IISGS), SERGAS-UVIGO, 32002 Ourense, Spain
| | - Ana Catarina Ribeiro
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
| | - Ricardo Dias
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
| | - Victor Freitas
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
| | - Susana Soares
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
| | - Rosa Pérez-Gregorio
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre 687, s/n, 4169-007 Porto, Portugal
- Food and Health Omics Group, Food and Agroecology Institute, University of Vigo, Campus As Lagoas, s/n, 32004 Ourense, Spain
- Food and Health Omics Group, Department of Chemistry and Biochemistry, Galicia Sur Health Research Institute (IISGS), SERGAS-UVIGO, 32002 Ourense, Spain
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11
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Das D, Sen V, Chakraborty G, Pillai V, Tambade R, Jonnalagadda PN, Rao AVSSN, Chittela RK. Quinaldine Red as a fluorescent probe for determining the melting temperature ( Tm) of proteins: a simple, rapid and high-throughput assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:950-956. [PMID: 38291911 DOI: 10.1039/d3ay01941a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Proteins play an important role in biological systems and several proteins are used in diagnosis, therapy, food industry etc. Thus, knowledge about the physical properties of the proteins is of utmost importance, which will aid in understanding their function and subsequent applications. The melting temperature (Tm) of a protein is one of the essential parameters which gives information about the stability of a protein under different conditions. In the present study, we have demonstrated a method for determining the Tm of proteins using the supramolecular interaction between Quinaldine Red (QR) and proteins. Using this method, we have determined the Tm of 5 proteins and compared our results with established protocols. Our results showed good agreement with the other methods and published values. The method developed in this study is inexpensive, quick, and devoid of complex instruments and pre/post-treatment of the samples. In addition, this method can be adopted for high throughput in multi-plate mode. Thus, this study projects a new methodology for Tm determination of various proteins with user friendly operation.
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Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Vikram Sen
- UM-DAE Centre for Excellence in Basic Sciences, Vidyanagari, Mumbai-400098, India
| | - Goutam Chakraborty
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai-400085, India
| | - Vinayaki Pillai
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Rahul Tambade
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Padma Nilaya Jonnalagadda
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai-400085, India
| | | | - Rajani Kant Chittela
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
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12
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Kotian NP, Prabhu A, Tender T, Raghu Chandrashekar H. Methylglyoxal Induced Modifications to Stabilize Therapeutic Proteins: A Review. Protein J 2024; 43:39-47. [PMID: 38017314 DOI: 10.1007/s10930-023-10166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
Therapeutic proteins are potent, fast-acting drugs that are highly effective in treating various conditions. Medicinal protein usage has increased in the past 10 years, and it will evolve further as we better understand disease molecular pathways. However, it is associated with high processing costs, limited stability, difficulty in being administered as an oral medication, and the inability of large proteins to penetrate tissue and reach their target locations. Many methods have been developed to overcome the problems with the stability and chaperone activity of therapeutic proteins, viz., the addition of external agents (changing the properties of the surrounding solvent by using stabilizing excipients, e.g., amino acids, sugars, polyols) and internal agents (chemical modifications that influence its structural properties, e.g., mutations, glycosylation). However, these methods must completely clear protein instability and chaperone issues. There is still much work to be done on finetuning chaperone proteins to increase their biological efficacy and stability. Methylglyoxal (MGO), a potent dicarbonyl compound, reacts with proteins and forms covalent cross-links. Much research on MGO scavengers has been conducted since they are known to alter protein structure, which may result in alterations in biological activity and stability. MGO is naturally produced within our body, however, its impact on chaperones and protein stability needs to be better understood and seems to vary based on concentration. This review highlights the efforts of several research groups on the effect of MGO on various proteins. It also addresses the impact of MGO on a client protein, α-crystallin, to understand the potential solutions to the protein's chaperone and stability problems.
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Affiliation(s)
- Nainika Prashant Kotian
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anusha Prabhu
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Tenzin Tender
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Hariharapura Raghu Chandrashekar
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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13
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Joy A, Biswas R. Significance of the Disulfide Bridge in the Structure and Stability of Metalloprotein Azurin. J Phys Chem B 2024; 128:973-984. [PMID: 38236012 DOI: 10.1021/acs.jpcb.3c07089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Metalloproteins make up a class of proteins that incorporate metal ions into their structures, enabling them to perform essential functions in biological systems, such as catalysis and electron transport. Azurin is one such metalloprotein with copper cofactor, having a β-barrel structure with exceptional thermal stability. The copper metal ion is coordinated at one end of the β-barrel structure, and there is a disulfide bond at the opposite end. In this study, we explore the effect of this disulfide bond in the high thermal stability of azurin by analyzing both the native S-S bonded and S-S nonbonded (S-S open) forms using temperature replica exchange molecular dynamics (REMD). Similar to experimental observations, we find a 35 K decrease in denaturation temperature for S-S open azurin compared to that of the native holo form (420 K). As observed in the case of native holo azurin, the unfolding process of the S-S open form also started with disruptions of the α-helix. The free energy surfaces of the unfolding process revealed that the denaturation event of the S-S open form progresses through different sets of conformational ensembles. Subsequently, we compared the stabilities of individual β-sheet strands of both the S-S bonded and the S-S nonbonded forms of azurin. Further, we examined the contacts between individual residues for the central structures from the free energy surfaces of the S-S nonbonded form. The microscopic origin of the lowering in the denaturation temperature is further supplemented by thermodynamic analysis.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu, Tirupati, Andhra Pradesh, India 517619
| | - Rajib Biswas
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu, Tirupati, Andhra Pradesh, India 517619
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14
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Xu B, Liang L, Jiang Y, Zhao Z. Investigating the ibrutinib resistance mechanism of L528W mutation on Bruton's tyrosine kinase via molecular dynamics simulations. J Mol Graph Model 2024; 126:108623. [PMID: 37716293 DOI: 10.1016/j.jmgm.2023.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/27/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Drug resistance to Bruton's Tyrosine Kinase (BTK) inhibitors presents a challenge in treating B-cell malignancies, and the mechanism behind drug resistance remains unclear. In this study, we focused on the BTK L528W mutation and investigated the underlying mechanisms of resistance to ibrutinib (including prototype and its active metabolite from, PCI-45227) using a combination of bioinformatics analysis, and molecular dynamics (MD) simulations. Protein stability of wild type (WT) BTK and L528W mutant was predicted using DUET, PoPMuSiC, and I-Mutant2.0. We performed MD simulations of six systems, apo-WT, metabolite-WT, prototype-WT and their mutants, to analyze the significant conformational and BTK-inhibitor binding affinity changes induced by the L528W mutation. Results show that the L528W mutation reduces the conformational stability of BTK compared to the WT. Principal component analysis (PCA) based free energy landscape (FEL) analysis shows that the L528W mutant ensemble tends to form more conformation clusters and exhibit higher levels of local minima than the WT counterpart. The interaction analysis reveal that the L528W mutation disrupts the strong hydrogen bond between Cys481 and inhibitors and reduces the number of hydrogen bonds between inhibitors and BTK in the L528W mutant complex structures compared to the WT. Porcupine plot analysis in association with cross-correlation analysis show the high-intensity flexible motion exhibited by the P-loop region. MM/GBSA calculations show that the L528W mutation in metabolite-BTK and prototype-BTK complexes increases binding free energy compared to the WT, with a reduction in binding affinity confirmed by per-residue energy decomposition. Specifically, the binding free energy increases from -57.86 kcal/mol to -48.26 kcal/mol for the metabolite-BTK complex and from -62.04 kcal/mol to -50.55 kcal/mol for the prototype-BTK complex. Overall, our study finds that the L528W mutation reduces BTK stability, decreases binding affinity, and leads to drug resistance and potential disease recurrence.
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Affiliation(s)
- Biyu Xu
- Department of Hematology, Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China; Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China
| | - Luguang Liang
- Department of Intensive Care Unit, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan City, 523710, Guangdong Province, China
| | - Yirong Jiang
- Department of Hematology, Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China; Dongguan Institute of Clinical Cancer Research, Dongguan Key Laboratory of Precision Diagnosis and Treatment for Tumors, Affiliated Dongguan Hospital, Southern Medical University, Dongguan City, 523050, Guangdong Province, China.
| | - Zuguo Zhao
- Department of Microbiology and Immunology of Basical Medicine of Guangdong Medical University, Dongguan City, 523808, Guangdong Province, China; Department of Intensive Care Unit, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan City, 523710, Guangdong Province, China.
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15
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Galano-Frutos JJ, Nerín-Fonz F, Sancho J. Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:7791-7806. [PMID: 37955428 PMCID: PMC10751793 DOI: 10.1021/acs.jcim.3c01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023]
Abstract
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. However, the challenge of calculating the state functions governing protein folding from first-principles remains unaddressed. We present here a simple approach that allows us to accurately calculate the energetics of protein folding. It is based on computing the energy of the folded and unfolded states at different temperatures using molecular dynamics simulations. From this, two essential quantities (ΔH and ΔCp) are obtained and used to calculate the conformational stability of the protein (ΔG). With this approach, we have successfully calculated the energetics of two- and three-state proteins, representatives of the major structural classes, as well as small stability differences (ΔΔG) due to changes in solution conditions or variations in an amino acid residue.
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Affiliation(s)
- Juan J. Galano-Frutos
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Francho Nerín-Fonz
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
| | - Javier Sancho
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
- Aragon
Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
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16
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Muellers SN, Allen KN, Whitty A. MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability. Proc Natl Acad Sci U S A 2023; 120:e2309884120. [PMID: 38039271 DOI: 10.1073/pnas.2309884120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation.
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Affiliation(s)
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215
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17
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Behairy MY, Eid RA, Otifi HM, Mohammed HM, Alshehri MA, Asiri A, Aldehri M, Zaki MSA, Darwish KM, Elhady SS, El-Shaer NH, Eldeen MA. Unraveling Extremely Damaging IRAK4 Variants and Their Potential Implications for IRAK4 Inhibitor Efficacy. J Pers Med 2023; 13:1648. [PMID: 38138875 PMCID: PMC10744719 DOI: 10.3390/jpm13121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Interleukin-1-receptor-associated kinase 4 (IRAK4) possesses a crucial function in the toll-like receptor (TLR) signaling pathway, and the dysfunction of this molecule could lead to various infectious and immune-related diseases in addition to cancers. IRAK4 genetic variants have been linked to various types of diseases. Therefore, we conducted a comprehensive analysis to recognize the missense variants with the most damaging impacts on IRAK4 with the employment of diverse bioinformatics tools to study single-nucleotide polymorphisms' effects on function, stability, secondary structures, and 3D structure. The residues' location on the protein domain and their conservation status were investigated as well. Moreover, docking tools along with structural biology were engaged in analyzing the SNPs' effects on one of the developed IRAK4 inhibitors. By analyzing IRAK4 gene SNPs, the analysis distinguished ten variants as the most detrimental missense variants. All variants were situated in highly conserved positions on an important protein domain. L318S and L318F mutations were linked to changes in IRAK4 secondary structures. Eight SNPs were revealed to have a decreasing effect on the stability of IRAK4 via both I-Mutant 2.0 and Mu-Pro tools, while Mu-Pro tool identified a decreasing effect for the G198E SNP. In addition, detrimental effects on the 3D structure of IRAK4 were also discovered for the selected variants. Molecular modeling studies highlighted the detrimental impact of these identified SNP mutant residues on the druggability of the IRAK4 ATP-binding site towards the known target inhibitor, HG-12-6, as compared to the native protein. The loss of important ligand residue-wise contacts, altered protein global flexibility, increased steric clashes, and even electronic penalties at the ligand-binding site interfaces were all suggested to be associated with SNP models for hampering the HG-12-6 affinity towards IRAK4 target protein. This given model lays the foundation for the better prediction of various disorders relevant to IRAK4 malfunction and sheds light on the impact of deleterious IRAK4 variants on IRAK4 inhibitor efficacy.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Hassan M. Otifi
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Heitham M. Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohammed A. Alshehri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Majed Aldehri
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohamed Samir A. Zaki
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nahla H. El-Shaer
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| | - Muhammad Alaa Eldeen
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
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18
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Al-nakhle HH, Yagoub HS, Anbarkhan SH, Alamri GA, Alsubaie NM. In Silico Evaluation of Coding and Non-Coding nsSNPs in the Thrombopoietin Receptor ( MPL) Proto-Oncogene: Assessing Their Influence on Protein Stability, Structure, and Function. Curr Issues Mol Biol 2023; 45:9390-9412. [PMID: 38132435 PMCID: PMC10742084 DOI: 10.3390/cimb45120589] [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: 10/23/2023] [Revised: 11/12/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The thrombopoietin receptor (MPL) gene is a critical regulator of hematopoiesis, and any alterations in its structure or function can result in a range of hematological disorders. Non-synonymous single nucleotide polymorphisms (nsSNPs) in MPL have the potential to disrupt normal protein function, prompting our investigation into the most deleterious MPL SNPs and the associated structural changes affecting protein-protein interactions. We employed a comprehensive suite of bioinformatics tools, including PredictSNP, InterPro, ConSurf, I-Mutant2.0, MUpro, Musitedeep, Project HOPE, STRING, RegulomeDB, Mutpred2, CScape, and CScape Somatic, to analyze 635 nsSNPs within the MPL gene. Among the analyzed nsSNPs, PredictSNP identified 28 as significantly pathogenic, revealing three critical functional domains within MPL. Ten of these nsSNPs exhibited high conservation scores, indicating potential effects on protein structure and function, while 14 were found to compromise MPL protein stability. Although the most harmful nsSNPs did not directly impact post-translational modification sites, 13 had the capacity to substantially alter the protein's physicochemical properties. Some mutations posed a risk to vital protein-protein interactions crucial for hematological functions, and three non-coding region nsSNPs displayed significant regulatory potential with potential implications for hematopoiesis. Furthermore, 13 out of 21 nsSNPs evaluated were classified as high-risk pathogenic variants by Mutpred2. Notably, amino acid alterations such as C291S, T293N, D295G, and W435C, while impactful on protein stability and function, were deemed non-oncogenic "passenger" mutations. Our study underscores the substantial impact of missense nsSNPs on MPL protein structure and function. Given MPL's central role in hematopoiesis, these mutations can significantly disrupt hematological processes, potentially leading to a variety of disorders. The identified high-risk pathogenic nsSNPs may hold promise as potential biomarkers or therapeutic targets for hematological diseases. This research lays the foundation for future investigations into the MPL gene's role in the realm of hematological health and diseases.
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Affiliation(s)
- Hakeemah H. Al-nakhle
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia; (H.S.Y.); (S.H.A.); (N.M.A.)
| | - Hind S. Yagoub
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia; (H.S.Y.); (S.H.A.); (N.M.A.)
- Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman 14415, Sudan
| | - Sadin H. Anbarkhan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia; (H.S.Y.); (S.H.A.); (N.M.A.)
| | - Ghadah A. Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia; (H.S.Y.); (S.H.A.); (N.M.A.)
| | - Norah M. Alsubaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Monawarah 42353, Saudi Arabia; (H.S.Y.); (S.H.A.); (N.M.A.)
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19
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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20
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Lee YT, Sickmier EA, Grigoriu S, Castro J, Boriack-Sjodin PA. Crystal structures of the DExH-box RNA helicase DHX9. Acta Crystallogr D Struct Biol 2023; 79:980-991. [PMID: 37860960 PMCID: PMC10619421 DOI: 10.1107/s2059798323007611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023] Open
Abstract
DHX9 is a DExH-box RNA helicase with versatile functions in transcription, translation, RNA processing and regulation of DNA replication. DHX9 has recently emerged as a promising target for oncology, but to date no mammalian structures have been published. Here, crystal structures of human, dog and cat DHX9 bound to ADP are reported. The three mammalian DHX9 structures share identical structural folds. Additionally, the overall architecture and the individual domain structures of DHX9 are highly conserved with those of MLE, the Drosophila orthologue of DHX9 previously solved in complex with RNA and a transition-state analogue of ATP. Due to differences in the bound substrates and global domain orientations, the localized loop conformations and occupancy of dsRNA-binding domain 2 (dsRBD2) differ between the mammalian DHX9 and MLE structures. The combined effects of the structural changes considerably alter the RNA-binding channel, providing an opportunity to compare active and inactive states of the helicase. Finally, the mammalian DHX9 structures provide a potential tool for structure-based drug-design efforts.
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Affiliation(s)
- Young-Tae Lee
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | | | - Simina Grigoriu
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
| | - Jennifer Castro
- Accent Therapeutics, 1050 Waltham Street, Lexington, MA 02421, USA
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21
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Hagströmer CJ, Hyld Steffen J, Kreida S, Al-Jubair T, Frick A, Gourdon P, Törnroth-Horsefield S. Structural and functional analysis of aquaporin-2 mutants involved in nephrogenic diabetes insipidus. Sci Rep 2023; 13:14674. [PMID: 37674034 PMCID: PMC10482962 DOI: 10.1038/s41598-023-41616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
Aquaporins are water channels found in the cell membrane, where they allow the passage of water molecules in and out of the cells. In the kidney collecting duct, arginine vasopressin-dependent trafficking of aquaporin-2 (AQP2) fine-tunes reabsorption of water from pre-urine, allowing precise regulation of the final urine volume. Point mutations in the gene for AQP2 may disturb this process and lead to nephrogenic diabetes insipidus (NDI), whereby patients void large volumes of highly hypo-osmotic urine. In recessive NDI, mutants of AQP2 are retained in the endoplasmic reticulum due to misfolding. Here we describe the structural and functional characterization of three AQP2 mutations associated with recessive NDI: T125M and T126M, situated close to a glycosylation site and A147T in the transmembrane region. Using a proteoliposome assay, we show that all three mutants permit the transport of water. The crystal structures of T125M and T126M together with biophysical characterization of all three mutants support that they retain the native structure, but that there is a significant destabilization of A147T. Our work provides unique molecular insights into the mechanisms behind recessive NDI as well as deepens our understanding of how misfolded proteins are recognized by the ER quality control system.
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Affiliation(s)
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Kreida
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tamim Al-Jubair
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Anna Frick
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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22
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Chapa-Villarreal FA, Miller M, Rodriguez-Cruz JJ, Pérez-Carlos D, Peppas NA. Self-assembled block copolymer biomaterials for oral delivery of protein therapeutics. Biomaterials 2023; 300:122191. [PMID: 37295223 DOI: 10.1016/j.biomaterials.2023.122191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Protein therapeutics have guided a transformation in disease treatment for various clinical conditions. They have been successful in numerous applications, but administration of protein therapeutics has been limited to parenteral routes which can decrease patient compliance as they are invasive and painful. In recent years, the synergistic relationship of novel biomaterials with modern protein therapeutics has been crucial in the treatment of diseases that were once thought of as incurable. This has guided the development of a variety of alternative administration routes, but the oral delivery of therapeutics remains one of the most desirable due to its ease of administration. This review addresses important aspects of micellar structures prepared by self-assembled processes with applications for oral delivery. These two characteristics have not been placed together in previous literature within the field. Therefore, we describe the barriers for delivery of protein therapeutics, and we concentrate in the oral/transmucosal pathway where drug carriers must overcome several chemical, physical, and biological barriers to achieve a successful therapeutic effect. We critically discuss recent research on biomaterials systems for delivering such therapeutics with an emphasis on self-assembled synthetic block copolymers. Polymerization methods and nanoparticle preparation techniques are similarly analyzed as well as relevant work in this area. Based on our own and others' research, we analyze the use of block copolymers as therapeutic carriers and their promise in treating a variety of diseases, with emphasis on self-assembled micelles for the next generation of oral protein therapeutic systems.
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Affiliation(s)
- Fabiola A Chapa-Villarreal
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin TX, USA
| | - Matthew Miller
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin TX, USA
| | - J Jesus Rodriguez-Cruz
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin TX, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Diego Pérez-Carlos
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin TX, USA
| | - Nicholas A Peppas
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin TX, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin TX, USA; Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
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23
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Hasan MM, Nabi AN, Yasmin T. Comprehensive analysis predicting effects of deleterious SNPs of human progesterone receptor gene on its structure and functions: a computational approach. J Biomol Struct Dyn 2023; 41:8002-8017. [PMID: 36166622 DOI: 10.1080/07391102.2022.2127908] [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: 07/22/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
Progesterone receptor plays a crucial role in the development of the mammary gland and breast cancer. Single nucleotide polymorphisms (SNPs) within its gene, PGR, are associated with the risk of miscarriages and preterm birth as well as many cancers across different populations. The main aim of this work is to investigate the most deleterious SNPs in the PGR gene to identify potential biomarkers for various disease susceptibility and treatments. Both sequence and structure-based computational approaches were adopted and in total 11 nsSNPs have been filtered out of 674 nsSNPs along with seven non-coding SNPs. R740Q, I744T and D746E belonged to a mutation cluster. R740Q, D746E along with S865L altered H-bond interactions within the receptor. The same mutations have been found to be associated with several cancers including uterine and breast cancer among others. It is, therefore, possible that the high-risk SNPs associated with cancers may exert their effect by causing changes in the protein structure, particularly in its bonding patterns, and thus affecting its function. In addition, seven non-coding SNPs that were located in the UTR region created a new miRNA site while three SNPs disrupted a conserved miRNA site. These high-risk SNPs can play an instrumental role in generating a dataset of the PGR gene's SNPs. Thus, the present study may pave the way to design and develop novel therapeutics for overcoming the challenges associated with certain cancers and pregnancy that result from a change in the protein structure and function due to the SNP mutations in the PGR gene.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Mahbub Hasan
- Population Genetics Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Ahm Nurun Nabi
- Population Genetics Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tahirah Yasmin
- Population Genetics Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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24
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Roy A, Paul I, Paul T, Hazarika K, Dihidar A, Ray S. An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2. J Biomol Struct Dyn 2023:1-29. [PMID: 37517062 DOI: 10.1080/07391102.2023.2239925] [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: 04/01/2023] [Accepted: 06/25/2023] [Indexed: 08/01/2023]
Abstract
DENV-2 strain is the most fatal and infectious of the five dengue virus serotypes. The non-structural protein NS1 encoded by its genome is the most significant protein required for viral pathogenesis and replication inside the host body. Thus, targeting the NS1 protein and designing an inhibitor to limit its stability and secretion is a propitious attempt in our fight against dengue. Four novel inhibitors are designed to target the conserved cysteine residues (C55, C313, C316, and C329) and glycosylation sites (N130 and N207) of the NS1 protein in an attempt to halt the spread of the dengue infection in the host body altogether. Numerous computer-aided drug designing techniques including molecular docking, molecular dynamics simulation, virtual screening, principal component analysis, and dynamic cross-correlation matrix were employed to determine the structural and functional activity of the NS1-inhibitor complexes. From our analysis, it was evident that the extent of structural and atomic level fluctuations of the ligand-bound protein exhibited a declining trend in contrast to unbound protein which was prominently noticeable through the RMSD, RMSF, Rg, and SASA graphs. The ADMET analysis of the four ligands revealed a promising pharmacokinetics and pharmacodynamic profile, along with good bioavailability and toxicity properties. The proposed drugs when bound to the targeted cavities resulted in stable conformations in comparison to their unbound state, implying they have good affinity promising effective drug action. Thus, they can be tested in vitro and used as potential anti-dengue drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Tanwi Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | | | - Aritrika Dihidar
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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25
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Barik S, Mahapatra A, Preeyanka N, Sarkar M. Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study. Phys Chem Chem Phys 2023; 25:20093-20108. [PMID: 37462948 DOI: 10.1039/d3cp01380d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.
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Affiliation(s)
- Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Amita Mahapatra
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Naupada Preeyanka
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
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26
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Zhang R, Akhtar N, Wani AK, Raza K, Kaushik V. Discovering Deleterious Single Nucleotide Polymorphisms of Human AKT1 Oncogene: An In Silico Study. Life (Basel) 2023; 13:1532. [PMID: 37511907 PMCID: PMC10381612 DOI: 10.3390/life13071532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND AKT1 is a serine/threonine kinase necessary for the mediation of apoptosis, angiogenesis, metabolism, and cell proliferation in both normal and cancerous cells. The mutations in the AKT1 gene have been associated with different types of cancer. Further, the AKT1 gene mutations are also reported to be associated with other diseases such as Proteus syndrome and Cowden syndromes. Hence, this study aims to identify the deleterious AKT1 missense SNPs and predict their effect on the function and structure of the AKT1 protein using various computational tools. METHODS Extensive in silico approaches were applied to identify deleterious SNPs of the human AKT1 gene and assessment of their impact on the function and structure of the AKT1 protein. The association of these highly deleterious missense SNPs with different forms of cancers was also analyzed. The in silico approach can help in reducing the cost and time required to identify SNPs associated with diseases. RESULTS In this study, 12 highly deleterious SNPs were identified which could affect the structure and function of the AKT1 protein. Out of the 12, four SNPs-namely, G157R, G159V, G336D, and H265Y-were predicted to be located at highly conserved residues. G157R could affect the ligand binding to the AKT1 protein. Another highly deleterious SNP, R273Q, was predicted to be associated with liver cancer. CONCLUSIONS This study can be useful for pharmacogenomics, molecular diagnosis of diseases, and developing inhibitors of the AKT1 oncogene.
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Affiliation(s)
- Ruojun Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Vikas Kaushik
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
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27
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Al-Nakhle HH, Khateb AM. Comprehensive In Silico Characterization of the Coding and Non-Coding SNPs in Human Dectin-1 Gene with the Potential of High-Risk Pathogenicity Associated with Fungal Infections. Diagnostics (Basel) 2023; 13:diagnostics13101785. [PMID: 37238269 DOI: 10.3390/diagnostics13101785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The human C-type lectin domain family 7 member A (CLEC7A) gene encodes a Dectin-1 protein that recognizes beta-1,3-linked and beta-1,6-linked glucans, which form the cell walls of pathogenic bacteria and fungi. It plays a role in immunity against fungal infections through pathogen recognition and immune signaling. This study aimed to explore the impact of nsSNPs in the human CLEC7A gene through computational tools (MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and PredictSNP) to identify the most deleterious and damaging nsSNPs. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-Mutant 2.0, ConSurf, and Project HOPE and post-translational modification analysis using MusiteDEEP. Out of the 28 nsSNPs that were found to be deleterious, 25 nsSNPs affected protein stability. Some SNPs were finalized for structural analysis with Missense 3D. Seven nsSNPs affected protein stability. Results from this study predicted that C54R, L64P, C120G, C120S, S135C, W141R, W141S, C148G, L155P, L155V, I158M, I158T, D159G, D159R, I167T, W180R, L183F, W192R, G197E, G197V, C220S, C233Y, I240T, E242G, and Y3D were the most structurally and functionally significant nsSNPs in the human CLEC7A gene. No nsSNPs were found in the predicted sites for post-translational modifications. In the 5' untranslated region, two SNPs, rs536465890 and rs527258220, showed possible miRNA target sites and DNA binding sites. The present study identified structurally and functionally significant nsSNPs in the CLEC7A gene. These nsSNPs may potentially be used for further evaluation as diagnostic and prognostic biomarkers.
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Affiliation(s)
- Hakeemah H Al-Nakhle
- Department of Medical Laboratory Technology, Collage of Applied Medical Science, Taibah University, Medina 42353, Saudi Arabia
| | - Aiah M Khateb
- Department of Medical Laboratory Technology, Collage of Applied Medical Science, Taibah University, Medina 42353, Saudi Arabia
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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28
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Abstract
Metal cofactors are critical centers for different biochemical processes of metalloproteins, and often, this metal coordination renders additional structural stability. In this study, we explore the additional stability conferred by the copper ion on azurin by analyzing both the apo and holo forms using temperature replica exchange molecular dynamics (REMD) data. We find a 14 K decrease in denaturation temperature for apo (406 K) azurin relative to that of holo (420 K), indicating a copper ion-induced additional thermal stability for holo azurin. The unfolding of apo azurin begins with the melting of α-helix and β-sheet V, similar to that of holo form. β-Sheets IV, VII, and VIII are comparatively more stable than other β-strands and melt at higher temperatures. Similar to holo azurin, the strong hydrophobic interactions among the apolar residues in the protein core is the key factor that renders high stability to apo protein as well. We construct free energy surfaces at different temperatures to capture the major conformations along the unfolding basins of the protein. Using contact maps from different basins we show the changes in the interaction between different residues along the unfolding pathway. Furthermore, we compare the Cα root-mean-square fluctuations (Cα-RMSF) and B-factor of all residues of apo and holo forms to understand the flexibility of different regions. The concerted displacement of α-helix and β-sheets V and VI from the protein core is another distinction we observe for apo compared to the holo form, where β-sheet VI was relatively stable.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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29
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Lisina S, Inam W, Huhtala M, Howaili F, Zhang H, Rosenholm JM. Nano Differential Scanning Fluorimetry as a Rapid Stability Assessment Tool in the Nanoformulation of Proteins. Pharmaceutics 2023; 15:pharmaceutics15051473. [PMID: 37242715 DOI: 10.3390/pharmaceutics15051473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
The development and production of innovative protein-based therapeutics is a complex and challenging avenue. External conditions such as buffers, solvents, pH, salts, polymers, surfactants, and nanoparticles may affect the stability and integrity of proteins during formulation. In this study, poly (ethylene imine) (PEI) functionalized mesoporous silica nanoparticles (MSNs) were used as a carrier for the model protein bovine serum albumin (BSA). To protect the protein inside MSNs after loading, polymeric encapsulation with poly (sodium 4-styrenesulfonate) (NaPSS) was used to seal the pores. Nano differential scanning fluorimetry (NanoDSF) was used to assess protein thermal stability during the formulation process. The MSN-PEI carrier matrix or conditions used did not destabilize the protein during loading, but the coating polymer NaPSS was incompatible with the NanoDSF technique due to autofluorescence. Thus, another pH-responsive polymer, spermine-modified acetylated dextran (SpAcDEX), was applied as a second coating after NaPSS. It possessed low autofluorescence and was successfully evaluated with the NanoDSF method. Circular dichroism (CD) spectroscopy was used to determine protein integrity in the case of interfering polymers such as NaPSS. Despite this limitation, NanoDSF was found to be a feasible and rapid tool to monitor protein stability during all steps needed to create a viable nanocarrier system for protein delivery.
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Affiliation(s)
- Sofia Lisina
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Wali Inam
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, 20500 Turku, Finland
| | - Fadak Howaili
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Jessica M Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
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30
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Jung F, Frey K, Zimmer D, Mühlhaus T. DeepSTABp: A Deep Learning Approach for the Prediction of Thermal Protein Stability. Int J Mol Sci 2023; 24:ijms24087444. [PMID: 37108605 PMCID: PMC10138888 DOI: 10.3390/ijms24087444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/04/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Proteins are essential macromolecules that carry out a plethora of biological functions. The thermal stability of proteins is an important property that affects their function and determines their suitability for various applications. However, current experimental approaches, primarily thermal proteome profiling, are expensive, labor-intensive, and have limited proteome and species coverage. To close the gap between available experimental data and sequence information, a novel protein thermal stability predictor called DeepSTABp has been developed. DeepSTABp uses a transformer-based protein language model for sequence embedding and state-of-the-art feature extraction in combination with other deep learning techniques for end-to-end protein melting temperature prediction. DeepSTABp can predict the thermal stability of a wide range of proteins, making it a powerful and efficient tool for large-scale prediction. The model captures the structural and biological properties that impact protein stability, and it allows for the identification of the structural features that contribute to protein stability. DeepSTABp is available to the public via a user-friendly web interface, making it accessible to researchers in various fields.
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Affiliation(s)
- Felix Jung
- Computational Systems Biology, RPTU University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Kevin Frey
- Computational Systems Biology, RPTU University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - David Zimmer
- Computational Systems Biology, RPTU University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU University of Kaiserslautern, 67663 Kaiserslautern, Germany
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31
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Khan S, Siraj S, Shahid M, Haque MM, Islam A. Osmolytes: Wonder molecules to combat protein misfolding against stress conditions. Int J Biol Macromol 2023; 234:123662. [PMID: 36796566 DOI: 10.1016/j.ijbiomac.2023.123662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
The proper functioning of any protein depends on its three dimensional conformation which is achieved by the accurate folding mechanism. Keeping away from the exposed stress conditions leads to cooperative unfolding and sometimes partial folding, forming the structures like protofibrils, fibrils, aggregates, oligomers, etc. leading to several neurodegenerative diseases like Parkinson's disease, Alzheimer's, Cystic fibrosis, Huntington, Marfan syndrome, and also cancers in some cases, too. Hydration of proteins is necessary, which may be achieved by the presence of organic solutes called osmolytes within the cell. Osmolytes belong to different classes in different organisms and play their role by preferential exclusion of osmolytes and preferential hydration of water molecules and achieves the osmotic balance in the cell otherwise it may cause problems like cellular infection, cell shrinkage leading to apoptosis and cell swelling which is also the major injury to the cell. Osmolyte interacts with protein, nucleic acids, intrinsically disordered proteins by non-covalent forces. Stabilizing osmolytes increases the Gibbs free energy of the unfolded protein and decreases that of folded protein and vice versa with denaturants (urea and guanidinium hydrochloride). The efficacy of each osmolyte with the protein is determined by the calculation of m value which reflects its efficiency with protein. Hence osmolytes can be therapeutically considered and used in drugs.
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Affiliation(s)
- Sobia Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Seerat Siraj
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, P.O. Box: 173, Al Kharj, Saudi Arabia
| | | | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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32
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Murty R, Bera MK, Walton IM, Whetzel C, Prausnitz MR, Walton KS. Interrogating Encapsulated Protein Structure within Metal-Organic Frameworks at Elevated Temperature. J Am Chem Soc 2023; 145:7323-7330. [PMID: 36961883 PMCID: PMC10080685 DOI: 10.1021/jacs.2c13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Encapsulating biomacromolecules within metal-organic frameworks (MOFs) can confer thermostability to entrapped guests. It has been hypothesized that the confinement of guest molecules within a rigid MOF scaffold results in heightened stability of the guests, but no direct evidence of this mechanism has been shown. Here, we present a novel analytical method using small-angle X-ray scattering (SAXS) to solve the structure of bovine serum albumin (BSA) while encapsulated within two zeolitic imidazolate frameworks (ZIF-67 and ZIF-8). Our approach comprises subtracting the scaled SAXS spectrum of the ZIF from that of the biocomposite BSA@ZIF to determine the radius of gyration of encapsulated BSA through Guinier, Kratky, and pair distance distribution function analyses. While native BSA exposed to 70 °C became denatured, in situ SAXS analysis showed that encapsulated BSA retained its size and folded state at 70 °C when encapsulated within a ZIF scaffold, suggesting that entrapment within MOF cavities inhibited protein unfolding and thus denaturation. This method of SAXS analysis not only provides insight into biomolecular stabilization in MOFs but may also offer a new approach to study the structure of other conformationally labile molecules in rigid matrices.
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Affiliation(s)
- Rohan Murty
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mrinal K Bera
- NSF's ChemMatCARS, Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Ian M Walton
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christina Whetzel
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark R Prausnitz
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Krista S Walton
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Wanarase SR, Chavan SV, Sharma S, D S. Evaluation of SNPs from human IGFBP6 associated with gene expression: an in-silico study. J Biomol Struct Dyn 2023; 41:13937-13949. [PMID: 36946206 DOI: 10.1080/07391102.2023.2192793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/28/2023] [Indexed: 03/23/2023]
Abstract
In the bloodstream and in local tissues, most IGF molecules are associated with the one of the members of the IGF-binding protein (IGFBP) family, which are divided into six distinct types. IGF-binding proteins have been demonstrated to either decrease or increase the growth-promoting effects of IGFs on cell culture, by extending their half-life. They alter how IGFs interact with the receptors on their cell surfaces. IGFBP6 gene is associated with disease in-situ carcinoma. Upregulation or downregulation of IGFBP6 gene has been implicated in different types of cancer in humans. Nonsynonymous SNPs changes have the potential to affect the protein's structure and function. Potential functional SNPs can be assessed before undertaking studies in larger populations because validation of these functional SNPs can be a crucial problem. So, in this in-silico investigation, we used a variety of sequence- and structure-based bioinformatics methods to separate the potential nsSNPs of the IGFBP6 gene from the neutral ones. In total of 216 nsSNPs, 5 were found to have potential effects using 5 prediction tools. From which, 2 nsSNPs (R128G and R164H) were selected as potentially damaging due to their presence in highly conserved region and ability to decrease protein stability. Among these 2 nsSNPs, only R164H was found to be associated with Uterine corpus endometrial carcinoma. It was also found that both, upregulation or downregulation of IGFBP6 gene can lead to the different types of cancers. The findings of the present study will certainly be valuable in the future large population-based investigations as well as drug discovery, especially developing personalized medicine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, Karnataka, India
| | - Susha D
- Department of Bioinformatics, BioNome, Bengaluru, Karnataka, India
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Williams SJ, Gewing-Mullins JA, Lieberman WK, Kolbaba-Kartchner B, Iqbal R, Burgess HM, Colee CM, Ornelas MY, Reid-McLaughlin ES, Mills JH, Prescher JA, Leconte AM. Biochemical Analysis Leads to Improved Orthogonal Bioluminescent Tools. Chembiochem 2023; 24:e202200726. [PMID: 36592373 PMCID: PMC10265744 DOI: 10.1002/cbic.202200726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/23/2022] [Accepted: 01/02/2023] [Indexed: 01/03/2023]
Abstract
Engineered luciferase-luciferin pairs have expanded the number of cellular targets that can be visualized in tandem. While light production relies on selective processing of synthetic luciferins by mutant luciferases, little is known about the origin of selectivity. The development of new and improved pairs requires a better understanding of the structure-function relationship of bioluminescent probes. In this work, we report a biochemical approach to assessing and optimizing two popular bioluminescent pairs: Cashew/d-luc and Pecan/4'-BrLuc. Single mutants derived from Cashew and Pecan revealed key residues for selectivity and thermal stability. Stability was further improved through a rational addition of beneficial residues. In addition to providing increased stability, the known stabilizing mutations surprisingly also improved selectivity. The resultant improved pair of luciferases are >100-fold selective for their respective substrates and highly thermally stable. Collectively, this work highlights the importance of mechanistic insight for improving bioluminescent pairs and provides significantly improved Cashew and Pecan enzymes which should be immediately suitable for multicomponent imaging applications.
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Affiliation(s)
- Sierra J Williams
- Department of Chemistry, University of California, Irvine, 1120 Natural Science II, Irvine, CA 92697, USA
| | - Jordan A Gewing-Mullins
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Whitney K Lieberman
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Bethany Kolbaba-Kartchner
- School of Molecular Sciences, Arizona State University, Physical Sciences Center PSd-D102, Tempe, AZ 85287, USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Reema Iqbal
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Hana M Burgess
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Clair M Colee
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Marya Y Ornelas
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Edison S Reid-McLaughlin
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
| | - Jeremy H Mills
- School of Molecular Sciences, Arizona State University, Physical Sciences Center PSd-D102, Tempe, AZ 85287, USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, 1120 Natural Science II, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Suite 100, Irvine, CA 92697, USA
| | - Aaron M Leconte
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, The Claremont Colleges, 925 N. Mills Ave., Claremont, CA 91711, USA
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N 6-methyladenosine of Spi2a attenuates inflammation and sepsis-associated myocardial dysfunction in mice. Nat Commun 2023; 14:1185. [PMID: 36864027 PMCID: PMC9979126 DOI: 10.1038/s41467-023-36865-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023] Open
Abstract
Bacteria-triggered sepsis is characterized by systemic, uncontrolled inflammation in affected individuals. Controlling the excessive production of pro-inflammatory cytokines and subsequent organ dysfunction in sepsis remains challenging. Here, we demonstrate that Spi2a upregulation in lipopolysaccharide (LPS)-stimulated bone marrow-derived macrophages reduces the production of pro-inflammatory cytokines and myocardial impairment. In addition, exposure to LPS upregulates the lysine acetyltransferase, KAT2B, to promote METTL14 protein stability through acetylation at K398, leading to the increased m6A methylation of Spi2a in macrophages. m6A-methylated Spi2a directly binds to IKKβ to impair IKK complex formation and inactivate the NF-κB pathway. The loss of m6A methylation in macrophages aggravates cytokine production and myocardial damage in mice under septic conditions, whereas forced expression of Spi2a reverses this phenotype. In septic patients, the mRNA expression levels of the human orthologue SERPINA3 negatively correlates with those of the cytokines, TNF, IL-6, IL-1β and IFNγ. Altogether, these findings suggest that m6A methylation of Spi2a negatively regulates macrophage activation in the context of sepsis.
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Miftahussurur M, Alfaray RI, Fauzia KA, Dewayani A, Doohan D, Waskito LA, Rezkitha YAA, Utomo DH, Somayana G, Fahrial Syam A, Lubis M, Akada J, Matsumoto T, Yamaoka Y. Low-grade intestinal metaplasia in Indonesia: Insights into the expression of proinflammatory cytokines during Helicobacter pylori infection and unique East-Asian CagA characteristics. Cytokine 2023; 163:156122. [PMID: 36640695 DOI: 10.1016/j.cyto.2022.156122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023]
Abstract
Helicobacter pylori infection is a major cause of intestinal metaplasia. In this study, we aimed to understand the reason underlying the low grade and incidence of intestinal metaplasia in Indonesia, based on the expression of genes encoding proinflammatory cytokines in gastric biopsy specimens. The possible reasons for the lesser virulence of the East-Asian-type CagA in Indonesia than that of the Western-type CagA, which is not common in other countries, were also investigated. The mRNA expression of cytokines was evaluated using real-time PCR. CagA characteristics were analyzed using in silico analysis. The expression of cytokines was typically not robust, among H. pylori-infected subjects in Indonesia, despite them predominantly demonstrating the East-Asian-type CagA. This might partially be explained by the characteristics of the East-Asian-type CagA in Indonesia, which showed a higher instability index and required higher energy to interact with proteins related to the cytokine induction pathway compared with the other types (p < 0.001 and p < 0.05, respectively). Taken together, besides the low prevalence of H. pylori, the low inflammatory response of the host and low CagA virulence, even among populations with high infection rates, may play an essential role in the low grade and low incidence of intestinal metaplasia in Indonesia. We believe that these findings would be relevant for better understanding of intestinal metaplasia, which is closely associated with the development of gastric cancer.
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Affiliation(s)
- Muhammad Miftahussurur
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Jalan Mayjend Prof, Dr. Moestopo, No. 6-8, Surabaya, Surabaya 60131, Indonesia; Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia.
| | - Ricky Indra Alfaray
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Kartika Afrida Fauzia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Astri Dewayani
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Infectious Disease Control, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Dalla Doohan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Physiology and Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia; Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Yudith Annisa Ayu Rezkitha
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Internal Medicine, Faculty of Medicine, University of Muhammadiyah, Surabaya, Surabaya 60113, Indonesia.
| | - Didik Huswo Utomo
- Research and Education Center for Bioinformatics, Indonesia Institute of Bioinformatics, Malang 65162, Indonesia.
| | - Gde Somayana
- Gastroentero Hepatology Division, Department of Internal Medicine, Faculty of Medicine-Sanglah Hospital, Udayana University, Denpasar, Bali 80114, Indonesia.
| | - Ari Fahrial Syam
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, University of Indonesia, Jakarta 10430, Indonesia.
| | - Masrul Lubis
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, Universitas Sumatera Utara, Medan 20222, Indonesia
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA.
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Mahapatra SR, Dey J, Raj TK, Misra N, Suar M. Designing a Next-Generation Multiepitope-Based Vaccine against Staphylococcus aureus Using Reverse Vaccinology Approaches. Pathogens 2023; 12:376. [PMID: 36986298 PMCID: PMC10058999 DOI: 10.3390/pathogens12030376] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Staphylococcus aureus is a human bacterial pathogen that can cause a wide range of symptoms. As virulent and multi-drug-resistant strains of S. aureus have evolved, invasive S. aureus infections in hospitals and the community have become one of the leading causes of mortality and morbidity. The development of novel techniques is therefore necessary to overcome this bacterial infection. Vaccines are an appropriate alternative in this context to control infections. In this study, the collagen-binding protein (CnBP) from S. aureus was chosen as the target antigen, and a series of computational methods were used to find epitopes that may be used in vaccine development in a systematic way. The epitopes were passed through a filtering pipeline that included antigenicity, toxicity, allergenicity, and cytokine inducibility testing, with the objective of identifying epitopes capable of eliciting both T and B cell-mediated immune responses. To improve vaccine immunogenicity, the final epitopes and phenol-soluble modulin α4 adjuvant were fused together using appropriate linkers; as a consequence, a multiepitope vaccine was developed. The chosen T cell epitope ensemble is expected to cover 99.14% of the global human population. Furthermore, docking and dynamics simulations were used to examine the vaccine's interaction with the Toll-like receptor 2 (TLR2), revealing great affinity, consistency, and stability between the two. Overall, the data indicate that the vaccine candidate may be extremely successful, and it will need to be evaluated in experimental systems to confirm its efficiency.
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Affiliation(s)
- Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
| | - T. Kiran Raj
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru 570015, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
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Ferreras S, Singh NP, Le Borgne R, Bun P, Binz T, Parton RG, Verbavatz JM, Vannier C, Galli T. A synthetic organelle approach to probe SNARE-mediated membrane fusion in a bacterial host. J Biol Chem 2023; 299:102974. [PMID: 36738791 PMCID: PMC10011478 DOI: 10.1016/j.jbc.2023.102974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
In vivo and in vitro assays, particularly reconstitution using artificial membranes, have established the role of synaptic soluble N-Ethylmaleimide-sensitive attachment protein receptors (SNAREs) VAMP2, Syntaxin-1A, and SNAP-25 in membrane fusion. However, using artificial membranes requires challenging protein purifications that could be avoided in a cell-based assay. Here, we developed a synthetic biological approach based on the generation of membrane cisternae by the integral membrane protein Caveolin in Escherichia coli and coexpression of SNAREs. Syntaxin-1A/SNAP-25/VAMP-2 complexes were formed and regulated by SNARE partner protein Munc-18a in the presence of Caveolin. Additionally, Syntaxin-1A/SNAP-25/VAMP-2 synthesis provoked increased length of E. coli only in the presence of Caveolin. We found that cell elongation required SNAP-25 and was inhibited by tetanus neurotoxin. This elongation was not a result of cell division arrest. Furthermore, electron and super-resolution microscopies showed that synaptic SNAREs and Caveolin coexpression led to the partial loss of the cisternae, suggesting their fusion with the plasma membrane. In summary, we propose that this assay reconstitutes membrane fusion in a simple organism with an easy-to-observe phenotype and is amenable to structure-function studies of SNAREs.
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Affiliation(s)
- Soledad Ferreras
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Neha Pratap Singh
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Remi Le Borgne
- Université Paris Cité, CNRS, UMR7592, Institut Jacques Monod, Paris, France
| | - Philippe Bun
- Université Paris Cité, NeurImag, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France
| | - Thomas Binz
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, Qld, Brisbane, Australia
| | | | - Christian Vannier
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France.
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France; GHU Paris psychiatrie neurosciences, Paris, France.
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Catalytic mechanism for Renilla-type luciferases. Nat Catal 2023. [DOI: 10.1038/s41929-022-00895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Nag A, Dasgupta A, Sengupta S, Lai TK, Acharya K. An in-silico pharmacophore-based molecular docking study to evaluate the inhibitory potentials of novel fungal triterpenoid Astrakurkurone analogues against a hypothetical mutated main protease of SARS-CoV-2 virus. Comput Biol Med 2023; 152:106433. [PMID: 36565483 PMCID: PMC9767885 DOI: 10.1016/j.compbiomed.2022.106433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/21/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The main protease is an important structural protein of SARS-CoV-2, essential for its survivability inside a human host. Considering current vaccines' limitations and the absence of approved therapeutic targets, Mpro may be regarded as the potential candidate drug target. Novel fungal phytocompound Astrakurkurone may be studied as the potential Mpro inhibitor, considering its medicinal properties reported elsewhere. METHODS In silico molecular docking was performed with Astrakurkurone and its twenty pharmacophore-based analogues against the native Mpro protein. A hypothetical Mpro was also constructed with seven mutations and targeted by Astrakurkurone and its analogues. Furthermore, multiple parameters such as statistical analysis (Principal Component Analysis), pharmacophore alignment, and drug likeness evaluation were performed to understand the mechanism of protein-ligand molecular interaction. Finally, molecular dynamic simulation was done for the top-ranking ligands to validate the result. RESULT We identified twenty Astrakurkurone analogues through pharmacophore screening methodology. Among these twenty compounds, two analogues namely, ZINC89341287 and ZINC12128321 showed the highest inhibitory potentials against native and our hypothetical mutant Mpro, respectively (-7.7 and -7.3 kcal mol-1) when compared with the control drug Telaprevir (-5.9 and -6.0 kcal mol-1). Finally, we observed that functional groups of ligands namely two aromatic and one acceptor groups were responsible for the residual interaction with the target proteins. The molecular dynamic simulation further revealed that these compounds could make a stable complex with their respective protein targets in the near-native physiological condition. CONCLUSION To conclude, Astrakurkurone analogues ZINC89341287 and ZINC12128321 can be potential therapeutic agents against the highly infectious SARS-CoV-2 virus.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Adhiraj Dasgupta
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Sutirtha Sengupta
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Tapan Kumar Lai
- Department of Chemistry, Vidyasagar Metropolitan College, Kolkata, West Bengal, India
| | - Krishnendu Acharya
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India.
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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Arora H, Dhiman D, Kumar K, Venkatesu P. Fortification of thermal and structural stability of hemoglobin using choline chloride-based deep eutectic solvents. Phys Chem Chem Phys 2022; 24:29683-29692. [PMID: 36453254 DOI: 10.1039/d2cp03407g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Of late, DESs have occupied the centre stage due to their eco-friendly and resource-efficient nature and their low toxicity. In this work, we have investigated the structural and thermal stability of hemoglobin (Hb) in two choline chloride ([Ch]Cl)-based DESs namely urea [Ch]Cl-urea (DES1) and [Ch]Cl-glycerol (Gly); (DES 2). Different biophysical techniques reveal that the presence of DESs facilitates the stability of Hb in a concentration-dependent manner and the extent of stability is more pronounced in [Ch]Cl-Gly as compared to [Ch]Cl-urea. Additionally, for a better understanding of the role of DESs in modulating the thermal and structural stability of Hb, studies have been performed on Hb in the presence of individual constituents of DESs, i.e., [Ch]Cl, urea, and Gly. Altogether, it was observed that the effect on the stability of Hb was by the presence of the DESs rather than their individual constituents. For instance, urea itself is a destabilizing co-solvent for biomolecules. However, the harmful effects of urea were surpassed when a DES is formed in the presence of [Ch]Cl. Therefore, overall, it can be concluded that both DESs can be described as potential non-harmful, green, and promising solvents for enhancing the structural and thermal stability of Hb.
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Affiliation(s)
- Harshita Arora
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
| | - Diksha Dhiman
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
| | - Krishan Kumar
- Department of Chemistry, University of Delhi, Delhi, 110 007, India. .,Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea
| | - Pannuru Venkatesu
- Department of Chemistry, University of Delhi, Delhi, 110 007, India.
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Behairy MY, Soltan MA, Eldeen MA, Abdulhakim JA, Alnoman MM, Abdel-Daim MM, Otifi H, Al-Qahtani SM, Zaki MSA, Alsharif G, Albogami S, Jafri I, Fayad E, Darwish KM, Elhady SS, Eid RA. HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility. Front Immunol 2022; 13:1008463. [PMID: 36569842 PMCID: PMC9780532 DOI: 10.3389/fimmu.2022.1008463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background A deep understanding of the causes of liability to SARS-CoV-2 is essential to develop new diagnostic tests and therapeutics against this serious virus in order to overcome this pandemic completely. In the light of the discovered role of antimicrobial peptides [such as human b-defensin-2 (hBD-2) and cathelicidin LL-37] in the defense against SARS-CoV-2, it became important to identify the damaging missense mutations in the genes of these molecules and study their role in the pathogenesis of COVID-19. Methods We conducted a comprehensive analysis with multiple in silico approaches to identify the damaging missense SNPs for hBD-2 and LL-37; moreover, we applied docking methods and molecular dynamics analysis to study the impact of the filtered mutations. Results The comprehensive analysis reveals the presence of three damaging SNPs in hBD-2; these SNPs were predicted to decrease the stability of hBD-2 with a damaging impact on hBD-2 structure as well. G51D and C53G mutations were located in highly conserved positions and were associated with differences in the secondary structures of hBD-2. Docking-coupled molecular dynamics simulation analysis revealed compromised binding affinity for hBD-2 SNPs towards the SARS-CoV-2 spike domain. Different protein-protein binding profiles for hBD-2 SNPs, in relation to their native form, were guided through residue-wise levels and differential adopted conformation/orientation. Conclusions The presented model paves the way for identifying patients prone to COVID-19 in a way that would guide the personalization of both the diagnostic and management protocols for this serious disease.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Mohamed A. Soltan
- Department of Microbiology and immunology, Faculty of Pharmacy, Sinai University – Kantara Branch, Ismailia, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Jawaher A. Abdulhakim
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Maryam M. Alnoman
- Biology Department, Faculty of Science, Taibah University, Yanbu, Saudi Arabia
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Hassan Otifi
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Saleh M. Al-Qahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia,Department of Histology and Cell Biology, College of Medicine, Zagazig University, Zagazig, Egypt
| | - Ghadi Alsharif
- College of Clinical Laboratory Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
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NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates. Essays Biochem 2022; 66:863-873. [PMID: 36416859 PMCID: PMC9760423 DOI: 10.1042/ebc20220056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022]
Abstract
The spatial and temporal organization of interactions between proteins underlie the regulation of most cellular processes. The requirement for such interactions to be specific predisposes a view that protein-protein interactions are relatively static and are formed through the stable complementarity of the interacting partners. A growing body of reports indicate, however, that many interactions lead to fuzzy complexes with an ensemble of conformations in dynamic exchange accounting for the observed binding. Here, we discuss how NMR has facilitated the characterization of these discrete, dynamic complexes and how such characterization has aided the understanding of dynamic, condensed phases of phase-separating proteins with exchanging multivalent interactions.
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In Silico Evaluation of Nonsynonymous SNPs in Human ADAM33: The Most Common Form of Genetic Association to Asthma Susceptibility. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1089722. [DOI: 10.1155/2022/1089722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/09/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022]
Abstract
ADAM33 is a zinc-dependent metalloprotease of the ADAM family, which plays a vital biological role as an activator of Th2 cytokines and growth factors. Moreover, this protein is crucial for the normal development of the lung in the fetus two months after gestation leading to determining lung functions all over life. In this regard, mutations in ADAM33 have been linked with asthma risk factors. Consequently, identifying ADAM33 pathogenic nonsynonymous single-nucleotide polymorphisms (nsSNPs) can be very important in asthma treatment. In the present study, 1055 nsSNPs of human ADAM33 were analyzed using biocomputational software, 31 of which were found to be detrimental mutations. Precise structural and stability analysis revealed D219V, C669G, and C606S as the most destabilizing SNPs. Furthermore, MD simulations disclosed higher overall fluctuation and alteration in intramolecular interactions compared with the wild-type structure. Overall, the results suggest D219V, C669G, and C606S detrimental mutations as a starting point for further case-control studies on the ADAM33 protein as well as an essential source for future targeted mechanisms.
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Liu X, Liang L, Wu B, Zhang X, Zeng X, Deng Y, Peng B, Zhang X, Zheng L. Effect of the R126C mutation on the structure and function of the glucose transporter GLUT1: A molecular dynamics simulation study. J Mol Graph Model 2022; 116:108227. [PMID: 35671570 DOI: 10.1016/j.jmgm.2022.108227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/14/2022]
Abstract
Glucose transporter 1 (GLUT1) is responsible for basal glucose uptake and is expressed in most tissues under normal conditions. GLUT1 mutations can cause early-onset absence epilepsy and myoclonus dystonia syndrome (MDS), with MDS potentially lethal. In this study, the effect of the R126C mutation, which is associated with MDS, on structural stability and substrate transport of GLUT1 was investigated. Various bioinformatics tools were used to predict the stability of GLUT1, revealing that the R126C mutation reduces the structural stability of GLUT1. Molecular dynamics (MD) simulations were used to further characterize the effect of the R126C mutation on GLUT1 structural stability. Based on the MD simulations, specific conformational changes and dominant motions of the GLUT1 mutant were characterized by Principal component analysis (PCA). The mutation disrupts hydrogen bonds between substrate-binding residues and glucose, thus likely reducing substrate affinity. The R126C mutation reduces the conformational stability of the protein, and fewer intramolecular hydrogen bonds were present in the mutated GLUT1 when compared with that of wild-type GLUT1. The mutation increased the free energy of glucose transport through GLUT1 significantly, especially at the mutation site, indicating that passage of glucose through the channel is hindered, and this mutant may even release cytoplasmic glucose. This study provides a detailed atomic-level explanation for the reduced structural stability and substrate transport capacity of a GLUT1 mutant. The results aid our understanding of the structure of GLUT1 and provide a framework for developing drugs to treat GLUT1-related diseases, such as MDS.
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Affiliation(s)
- Xiaoliu Liu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Medical Laboratory of Shenzhen Luohu People's Hospital, 518001, China
| | - Luguang Liang
- School of Laboratory Medicine, Guangdong Medical University, Dongguan, China
| | - Bodeng Wu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xin Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | | | - Yurong Deng
- Medical Laboratory of Shenzhen Luohu People's Hospital, 518001, China
| | - Bin Peng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiuming Zhang
- Medical Laboratory of Shenzhen Luohu People's Hospital, 518001, China.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Muindi MP, Lee JH, Kweon H, Kasina M. Effect of Extraction Ingredients on the Conformation and Stability of Silk Sericin (SS). Polymers (Basel) 2022; 14:polym14194118. [PMID: 36236065 PMCID: PMC9572401 DOI: 10.3390/polym14194118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Silk sericin (SS) has different physicochemical properties depending on the extraction technique. In this study, SS was isolated in the presence of ingredients, including 5 to 10% ethanol (EtOH) and 5 to 10% glycine. Furthermore, temperature conditions of 80 °C, 100 °C, and 120 °C were used for 1, 3, and 5 h to evaluate the extraction rates. The extraction, gelation, structural, and cytotoxicity properties of SS extracted under different conditions were investigated. Extraction at 100 °C and 120 °C were found to have the highest SS yield, with 80 °C being the lowest. SS isolated at 100 °C and 120 °C for 1 and 3 h in water, and EtOH gelled at 4 °C in 2 to 3 days and 37 °C in 40 min. Glycine SS extracts were obtained at 100 °C and 120 °C for 1 h, gelled at 4 °C for 20 days and 37 °C for 16 h. SS was observed at 80 °C, with no gelation occurring. Glycine SS extracts obtained for 3, and 5 h at 120 °C showed no gelation. Circular dichroism (CD) results show glycine in SS induces α-helix and random coil structure. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and fast performance liquid chromatography (FPLC) were used to quantify the molecular weight distribution at 63 and 70 kDa, respectively. The MMT assay (3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) revealed no cytotoxicity in macrophage RAW 264.7 cells treated with this method SS; these findings present the significance and possibility of using selected extraction ingredients in SS that allow for the application of native SS at an initial extraction viscosity.
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Affiliation(s)
- Munguti Peter Muindi
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
| | - Ji Hae Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - HaeYong Kweon
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - Muo Kasina
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
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Ionic liquids as protein stabilizers for biological and biomedical applications: A review. Biotechnol Adv 2022; 61:108055. [DOI: 10.1016/j.biotechadv.2022.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022]
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Behairy MY, Abdelrahman AA, Toraih EA, Ibrahim EEDA, Azab MM, Sayed AA, Hashem HR. Investigation of TLR2 and TLR4 Polymorphisms and Sepsis Susceptibility: Computational and Experimental Approaches. Int J Mol Sci 2022; 23:ijms231810982. [PMID: 36142893 PMCID: PMC9504743 DOI: 10.3390/ijms231810982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Toll-like receptors (TLR) play an eminent role in the regulation of immune responses to invading pathogens during sepsis. TLR genetic variants might influence individual susceptibility to developing sepsis. The current study aimed to investigate the association of genetic polymorphisms of the TLR2 and TLR4 with the risk of developing sepsis with both a pilot study and in silico tools. Different in silico tools were used to predict the impact of our SNPs on protein structure, stability, and function. Furthermore, in our prospective study, all patients matching the inclusion criteria in the intensive care units (ICU) were included and followed up, and DNA samples were genotyped using real-time polymerase chain reaction (RT-PCR) technology. There was a significant association between TLR2 Arg753Gln polymorphisms and sepsis under the over-dominant model (p = 0.043). In contrast, we did not find a significant difference with the TLR4 Asp299Gly polymorphism with sepsis. However, there was a significant association between TLR4 Asp299Gly polymorphisms and Acinetobacter baumannii infection which is quite a virulent organism in ICU (p = 0.001) and post-surgical cohorts (p = 0.033). Our results conclude that the TLR2 genotype may be a risk factor for sepsis in adult patients.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32958, Egypt
| | - Ali A. Abdelrahman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Eman A. Toraih
- Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA
- Genetics Unit, Department of Histology & Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Emad El-Deen A. Ibrahim
- Department of Anesthesia, Intensive Care and Pain Management, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Marwa M. Azab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (M.M.A.); (A.A.S.); Tel.: +20-10-2429-9630 (M.M.A.); +966-14-861-8888 (A.A.S.)
| | - Anwar A. Sayed
- Department of Medical Microbiology and Immunology, Taibah University, Madinah 42353, Saudi Arabia
- Department of Surgery and Cancer, Imperial College London, London SW7 2BX, UK
- Correspondence: (M.M.A.); (A.A.S.); Tel.: +20-10-2429-9630 (M.M.A.); +966-14-861-8888 (A.A.S.)
| | - Hany R. Hashem
- Department of Microbiology and Immunology, Faculty of Pharmacy, Fayoum University, Fayoum 63514, Egypt
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Lee S, Jo K, Jeong HG, Choi YS, Kyoung H, Jung S. Freezing-induced denaturation of myofibrillar proteins in frozen meat. Crit Rev Food Sci Nutr 2022; 64:1385-1402. [PMID: 36052640 DOI: 10.1080/10408398.2022.2116557] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.
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Affiliation(s)
- Seonmin Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Kyung Jo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Hyun Gyung Jeong
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Yun-Sang Choi
- Research Group of Food Processing, Korea Food Research Institute, Wanju, Korea
| | - Hyunjin Kyoung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Samooel Jung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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