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Sequeiros-Borja C, Surpeta B, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J. Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. J Chem Inf Model 2024; 64:6014-6025. [PMID: 38669675 PMCID: PMC11323245 DOI: 10.1021/acs.jcim.4c00094] [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: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at the molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or by functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein's tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with subangstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for the relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.
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Affiliation(s)
- Carlos Sequeiros-Borja
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Bartlomiej Surpeta
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Aravind Selvaram Thirunavukarasu
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | | | - Igor Marchlewski
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
| | - Jan Brezovsky
- International
Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
- Laboratory
of Biomolecular Interactions and Transport, Department of Gene Expression,
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań 61-614, Poland
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2
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Killian JT, Glenn King R, Lucander ACK, Kizziah JL, Fucile CF, Diaz-Avalos R, Qiu S, Silva-Sanchez A, Mousseau BJ, Macon KJ, Callahan AR, Yang G, Emon Hossain M, Akther J, Good DB, Kelso S, Houp JA, Rosenblum F, Porrett PM, Ong SC, Kumar V, Saphire EO, Kearney JF, Randall TD, Rosenberg AF, Green TJ, Lund FE. HLA topography enforces shared and convergent immunodominant B cell and antibody alloresponses in transplant recipients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.31.534734. [PMID: 37034637 PMCID: PMC10081326 DOI: 10.1101/2023.03.31.534734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Donor-specific antibody (DSA) responses against human leukocyte antigen (HLA) proteins mismatched between kidney transplant donors and recipients cause allograft loss. The rules governing the immunogenicity of non-self donor HLA are poorly understood. Using single-cell, molecular, structural, and proteomic techniques, we profiled the HLA-specific B cell response in the kidney and blood of a transplant recipient with antibody-mediated rejection (AMR). We observed an immunodominant B cell antibody response focused on topographically exposed, solvent-accessible mismatched HLA residues along the peptide-binding groove - a subregion comprising only 20% of the HLA molecule. We further demonstrated that, even within a diverse cohort of transplant recipients, the B cell alloresponse consistently converges on this same immunodominant subregion on the crown of the HLA molecule. Based on these findings, we propose that B cell immunodominance in transplant rejection relies on antigenic topography, and we suggest that this link could be exploited for organ matching and therapeutics.
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3
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Rybak MY, Gagnon MG. Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Nat Struct Mol Biol 2024; 31:810-816. [PMID: 38538914 DOI: 10.1038/s41594-024-01236-3] [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: 02/28/2023] [Accepted: 01/31/2024] [Indexed: 04/18/2024]
Abstract
The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 104 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNAIleCAU (tRNAIleCAU). Bacterial tRNAIleCAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNAIleLAU in the process of decoding AUA and AUG. Lysidine in tRNAIleLAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNAIleLAU specifically decodes AUA over AUG.
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MESH Headings
- Peptide Elongation Factor Tu/metabolism
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/genetics
- Cryoelectron Microscopy
- Escherichia coli/metabolism
- Escherichia coli/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Ribosomes/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- Models, Molecular
- Codon/metabolism
- Codon/genetics
- Anticodon/chemistry
- Anticodon/metabolism
- Nucleic Acid Conformation
- Isoleucine/metabolism
- Isoleucine/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Lysine/analogs & derivatives
- Pyrimidine Nucleosides
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Affiliation(s)
- Mariia Yu Rybak
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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4
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Hanafiah A, Abd Aziz SNA, Md Nesran ZN, Wezen XC, Ahmad MF. Molecular investigation of antimicrobial peptides against Helicobacter pylori proteins using a peptide-protein docking approach. Heliyon 2024; 10:e28128. [PMID: 38533069 PMCID: PMC10963377 DOI: 10.1016/j.heliyon.2024.e28128] [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: 08/14/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
The impact of H. pylori resistance on patient's treatment failure is a major concern. Therefore, the development of novel or alternative therapies for H. pylori is urgently needed. The purpose of this study was to investigate the molecular interactions of various antimicrobial peptides (AMPs) to H. pylori proteins. We performed the peptide-protein molecular docking using HADDOCK 2.4 webserver. Fourteen AMPs were tested for their binding efficacy against four H. pylori proteins. Simulation of the peptide-protein complex was performed using molecular dynamic software package AMBER20. From molecular docking analysis, five peptides (LL-37, Tilapia piscidin 4, napin, snakin-1 and EcAMP1) showed strong binding interactions against H. pylori proteins. The strongest binding affinity was observed in the interactions between Snakin-1 and PBP2, TP4 and type I HopQ and EcAMP1 and type I HopQ with -11.1, -13.6 and -13.8 kcal/mol, respectively. The dynamic simulation was performed for two complexes (snakin1-PBP2 and EcAMP1-HopQ). Results of the dynamics simulation showed that EcAMP1 had stable interaction and binding to type I HopQ protein without significant structural changes. In conclusion, both results of docking and simulation showed that EcAMP1 might be useful as a potential therapeutic agent for H. pylori treatment. This molecular approach provides deep understanding of the interaction insights between AMPs and H. pylori proteins. It paves the way for the development of novel anti-H. pylori using antimicrobial peptides.
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Affiliation(s)
- Alfizah Hanafiah
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
- GUT Research Group, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Siti Nur Arifah Abd Aziz
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Zarith Nameyrra Md Nesran
- Dept. of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Xavier Chee Wezen
- School of Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology, 93350, Kuching, Sarawak, Malaysia
| | - Mohd Fadzli Ahmad
- Faculty of Engineering and Life Sciences, Universiti Selangor, 45600, Bestari Jaya, Selangor, Malaysia
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5
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Amangeldina A, Tan ZW, Berezovsky IN. Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation. Curr Res Struct Biol 2024; 7:100129. [PMID: 38327713 PMCID: PMC10847869 DOI: 10.1016/j.crstbi.2024.100129] [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: 11/29/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.
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Affiliation(s)
- Aidana Amangeldina
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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6
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Cheng CW, Wu CY, Wang SW, Chen JY, Kung CC, Liao KS, Wong CH. Low-sugar universal mRNA vaccine against coronavirus variants with deletion of glycosites in the S2 or stem of SARS-CoV-2 spike messenger RNA (mRNA). Proc Natl Acad Sci U S A 2023; 120:e2314392120. [PMID: 38011546 DOI: 10.1073/pnas.2314392120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Since the outbreak of Severe Acute Respiratory Syndrome Virus-2 (SARS-CoV-2) in 2019, more than 15 million spike protein sequences have been identified, raising a new challenge for the development of a broadly protective vaccine against the various emerging variants. We found that the virus, like most other human viruses, depends on host-made glycans to shield the conserved epitopes on spike protein from immune response and demonstrated that deletion of the glycan shields exposed highly conserved epitopes and elicited broadly protective immune responses. In this study, we identified 17 conserved epitopes from 14 million spike protein sequences and 11 of the conserved epitopes are in the S2 domain, including the six most conserved epitopes in the stem region. We also demonstrated that deletion of the glycosites in the spike messenger RNA (mRNA) S2 domain or the stem region exposed the highly conserved epitopes and elicited broadly protective immune responses, particularly CD-8+ T cell response against various SARS-CoV-2 variants, and other human coronaviruses including MERS, SARS viruses, and those causing common cold.
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Affiliation(s)
- Cheng-Wei Cheng
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
- The Master Program of AI Application in Health Industry, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan
- Center for Big Data Research, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung City 80708, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
- Rock BioMedical, Inc., Taipei City 115202, Taiwan
| | - Szu-Wen Wang
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
- Rock BioMedical, Inc., Taipei City 115202, Taiwan
| | - Jia-Yan Chen
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
| | - Chih-Chuan Kung
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
| | - Kuo-Shiang Liao
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
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7
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Yamamoto K, Nagatoishi S, Matsunaga R, Nakakido M, Kuroda D, Tsumoto K. Conformational features and interaction mechanisms of V H H antibodies with β-hairpin CDR3: A case of Nb8-HigB2 interaction. Protein Sci 2023; 32:e4827. [PMID: 37916305 PMCID: PMC10661080 DOI: 10.1002/pro.4827] [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: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
The β-hairpin conformation is regarded as an important basic motif to form and regulate protein-protein interactions. Single-domain VH H antibodies are potential therapeutic and diagnostic tools, and the third complementarity-determining regions of the heavy chains (CDR3s) of these antibodies are critical for antigen recognition. Although the sequences and conformations of the CDR3s are diverse, CDR3s sometimes adopt β-hairpin conformations. However, characteristic features and interaction mechanisms of β-hairpin CDR3s remain to be fully elucidated. In this study, we investigated the molecular recognition of the anti-HigB2 VH H antibody Nb8, which has a CDR3 that forms a β-hairpin conformation. The interaction was analyzed by evaluation of alanine-scanning mutants, molecular dynamics simulations, and hydrogen/deuterium exchange mass spectrometry. These experiments demonstrated that positions 93 and 94 (Chothia numbering) in framework region 3, which is right outside CDR3 by definition, play pivotal roles in maintaining structural stability and binding properties of Nb8. These findings will facilitate the design and optimization of single-domain antibodies.
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Affiliation(s)
- Koichi Yamamoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
| | - Ryo Matsunaga
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Kuroda
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
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8
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Alba-Posse EJ, Bruque CD, Gándola Y, Gasulla J, Nadra AD. From in-silico screening to in-vitro evaluation: Enhancing the detection of Microcystins with engineered PP1 mutant variants. J Struct Biol 2023; 215:108043. [PMID: 37935286 DOI: 10.1016/j.jsb.2023.108043] [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: 07/15/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023]
Abstract
Cyanotoxins produced during harmful algal blooms (CyanoHABs) have become a worldwide issue of concern. Microcystins (MC) are the most ubiquitous group of cyanotoxins and have known carcinogenic and hepatotoxic effects. The protein phosphatase inhibition assays (PPIAs), based on the inhibition of Protein Phosphatase 1/2A (PP1/PP2A) by MC, are one of the most cost-effective options for detecting MC. In this work, we aimed to design in-silico and evaluate in-vitro mutant variants of the PP1 protein, in order to enhance their capabilities as a MC biosensor. To this end, we performed an in-silico active site-saturated mutagenesis screening, followed by stability and docking affinity calculation with the MCLR cyanotoxin. Candidates with improved both affinity and stability were further tested in a fully flexible active-site docking. The best-scored mutations (19) were individually analysed regarding their locations and interactions. Four of them (p.D197F; p.Q249Y; p.S129W; p.D220Q) were selected for in-vitro expression and evaluation. Mutant p.D197F, exhibited a significant increment in inhibition by MCLR with respect to the WT, while showing a non-significant difference in stability nor activity. This successful PP1 inhibition enhancement suggests the potential of the p.D197F variant for practical MC detection applications.
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Affiliation(s)
- Ezequiel J Alba-Posse
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina
| | - Carlos David Bruque
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina; Unidad de Conocimiento Traslacional Hospitalaria Patagónica, Hospital de Alta Complejidad El Calafate - S.A.M.I.C., Jorge Newbery 453, CP9405 El Calafate, Santa Cruz, Argentina
| | - Yamila Gándola
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina
| | - Javier Gasulla
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina.
| | - Alejandro D Nadra
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina.
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9
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Willems A, Kalaw A, Ecer A, Kotwal A, Roepe LD, Roepe PD. Structures of Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) Isoforms and Their Interactions with Chloroquine. Biochemistry 2023; 62:1093-1110. [PMID: 36800498 PMCID: PMC10950298 DOI: 10.1021/acs.biochem.2c00669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Indexed: 02/19/2023]
Abstract
Using a recently elucidated atomic-resolution cryogenic electron microscopy (cryo-EM) structure for the Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein 7G8 isoform as template [Kim, J.; Nature 2019, 576, 315-320], we use Monte Carlo molecular dynamics (MC/MD) simulations of PfCRT embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane to solve energy-minimized structures for 7G8 PfCRT and two additional PfCRT isoforms that harbor 5 or 7 amino acid substitutions relative to 7G8 PfCRT. Guided by drug binding previously defined using chloroquine (CQ) photoaffinity probe labeling, we also use MC/MD energy minimization to elucidate likely CQ binding geometries for the three membrane-embedded isoforms. We inventory salt bridges and hydrogen bonds in these structures and summarize how the limited changes in primary sequence subtly perturb local PfCRT isoform structure. In addition, we use the "AlphaFold" artificial intelligence AlphaFold2 (AF2) algorithm to solve for domain structure that was not resolved in the previously reported 7G8 PfCRT cryo-EM structure, and perform MC/MD energy minimization for the membrane-embedded AF2 structures of all three PfCRT isoforms. We compare energy-minimized structures generated using cryo-EM vs AF2 templates. The results suggest how amino acid substitutions in drug resistance-associated isoforms of PfCRT influence PfCRT structure and CQ transport.
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Affiliation(s)
| | | | - Ayse Ecer
- Departments of Chemistry
and Biochemistry and Cellular and Molecular Biology, Georgetown University, 37th and O Streets NW, Washington, District of Columbia 20057, United States
| | - Amitesh Kotwal
- Departments of Chemistry
and Biochemistry and Cellular and Molecular Biology, Georgetown University, 37th and O Streets NW, Washington, District of Columbia 20057, United States
| | | | - Paul D. Roepe
- Departments of Chemistry
and Biochemistry and Cellular and Molecular Biology, Georgetown University, 37th and O Streets NW, Washington, District of Columbia 20057, United States
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10
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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11
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Altunayar-Unsalan C, Unsalan O, Mavromoustakos T. Molecular interactions of hesperidin with DMPC/cholesterol bilayers. Chem Biol Interact 2022; 366:110131. [PMID: 36037876 DOI: 10.1016/j.cbi.2022.110131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
Since cell membranes are complex systems, the use of model lipid bilayers is quite important for the study of their interactions with bioactive molecules. Mammalian cell membranes require cholesterol (CHOL) for their structure and function. For this reason, the mixtures of phospholipid and cholesterol are necessary to use in model membrane studies to better simulate the real systems. In the present study, we investigated the effect of the incorporation of hesperidin in model membranes consisting of dimyristoylphosphatidylcholine (DMPC) and CHOL by using differential scanning calorimetry (DSC), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and atomic force microscopy (AFM). ATR-FTIR results demonstrated that hesperidin increases the fluidity of the DMPC/CHOL binary system. DSC findings indicated that the presence of 5 mol% hesperidin induces a broadening of the main phase transition consisting of three overlapping components. AFM experiments showed that hesperidin increases the thickness of DMPC/CHOL lipid bilayer model membranes. In addition to experimental results, molecular docking studies were conducted with hesperidin and human lanosterol synthase (LS), which is an enzyme found in the final step of cholesterol synthesis, to characterize hesperidin's interactions with its surrounding via its hydroxyl and oxygen groups. Then, hesperidin's ADME/Tox (absorption, distribution, metabolism, excretion and toxicity) profile was computed to see the potential impact on living system. In conclusion, considering the data obtained from experimental studies, this work ensures molecular insights in the interaction between a flavonoid, as an antioxidant drug model, and lipids mimicking those found in mammalian membranes. Moreover, computational studies demonstrated that hesperidin may be a great potential for use as a therapeutic agent for hypercholesterolemia due to its antioxidant property.
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Affiliation(s)
- Cisem Altunayar-Unsalan
- Ege University Central Research Testing and Analysis Laboratory Research and Application Center, 35100, Bornova, Izmir, Turkey.
| | - Ozan Unsalan
- Ege University, Faculty of Science, Department of Physics, 35100, Bornova, Izmir, Turkey.
| | - Thomas Mavromoustakos
- Section of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece.
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12
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Khan AS, Parvez N, Ahsan T, Shoily SS, Sajib AA. A comprehensive in silico exploration of the impacts of missense variants on two different conformations of human pirin protein. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:225. [PMID: 35967515 PMCID: PMC9362109 DOI: 10.1186/s42269-022-00917-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pirin, a member of the cupin superfamily, is an iron-binding non-heme protein. It acts as a coregulator of several transcription factors, especially the members of NFκB transcription factor family. Based on the redox state of its iron cofactor, it can assume two different conformations and thereby act as a redox sensor inside the nucleus. Previous studies suggested that pirin may be associated with cancer, inflammatory diseases as well as COVID-19 severities. Hence, it is important to explore the pathogenicity of its missense variants. In this study, we used a number of in silico tools to investigate the effects of missense variants of pirin on its structure, stability, metal cofactor binding affinity and interactions with partner proteins. In addition, we used protein dynamics simulation to elucidate the effects of selected variants on its dynamics. Furthermore, we calculated the frequencies of haplotypes containing pirin missense variants across five major super-populations (African, Admixed American, East Asian, European and South Asian). RESULTS Among a total of 153 missense variants of pirin, 45 were uniformly predicted to be pathogenic. Of these, seven variants can be considered for further experimental studies. Variants R59P and L116P were predicted to significantly destabilize and damage pirin structure, substantially reduce its affinity to its binding partners and alter pirin residue fluctuation profile via changing the flexibility of several key residues. Additionally, variants R59Q, F78V, G98D, V151D and L220P were found to impact pirin structure and function in multiple ways. As no haplotype was identified to be harboring more than one missense variant, further interrogation of the individual effects of these seven missense variants is highly recommended. CONCLUSIONS Pirin is involved in the transcriptional regulation of several genes and can play an important role in inflammatory responses. The variants predicted to be pathogenic in this study may thus contribute to a better understanding of the underlying molecular mechanisms of various inflammatory diseases. Future studies should be focused on clarifying if any of these variants can be used as disease biomarkers. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-022-00917-7.
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Affiliation(s)
- Auroni Semonti Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, 1100 Bangladesh
| | - Nahid Parvez
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, 1100 Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349 Bangladesh
| | - Sabrina Samad Shoily
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000 Bangladesh
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13
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Badonyi M, Marsh JA. Large protein complex interfaces have evolved to promote cotranslational assembly. eLife 2022; 11:79602. [PMID: 35899946 PMCID: PMC9365393 DOI: 10.7554/elife.79602] [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: 04/20/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromeric subunits in bacterial, yeast, and human complexes. When considering all together, we observe the N-terminal interface to be larger than the C-terminal interface 54% of the time, increasing to 64% when we exclude subunits with only small interfaces, which are unlikely to cotranslationally assemble. This strongly suggests that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
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Affiliation(s)
- Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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14
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Mteremko D, Shadrack DM, Ntie-Kang F, Chilongola J, Chacha M. Finding alternatives to 5-fluorouracil: application of ensemble-based virtual screening for drug repositioning against human thymidylate synthase. J Biomol Struct Dyn 2022:1-17. [PMID: 35538714 DOI: 10.1080/07391102.2022.2074140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
5-fluorouracil and analogs are used in the treatment of many solid tumours. However, there are many cases of resistance and high toxicity associated with 5-fluorouracil chemotherapy. Repurposing FDA drugs against human thymidylate synthase revealed a number of FDA drugs that have a potential to be further developed for the treatment of various cancers for which 5-fluorouracil and analogs have been used for chemotherapy. Four FDA drugs prioritized for further validation included Erismodegib, Irinotecan, Conivaptan and Ergotamine. The role of water in mediating drug interactions and its contribution to the total binding energy was also shown. MM-PBSA calculations revealed that the binding affinity was the lowest for the hTS-Ergotamine complex (-66.702 ± 1.807 kJ/mol) suggesting moderate inhibition despite a large energetic contribution from van der Waal interactions (-190.889 ± 1.027 kJ/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Denis Mteremko
- Global Health and Biomedical Sciences, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | - Jaffu Chilongola
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Musa Chacha
- Global Health and Biomedical Sciences, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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15
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Trozzi F, Karki N, Song Z, Verma N, Kraka E, Zoltowski BD, Tao P. Allosteric control of ACE2 peptidase domain dynamics. Org Biomol Chem 2022; 20:3605-3618. [PMID: 35420112 PMCID: PMC9205182 DOI: 10.1039/d2ob00606e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Angiotensin Converting Enzyme 2 (ACE2) assists the regulation of blood pressure and is the main target of the coronaviruses responsible for SARS and COVID19. The catalytic function of ACE2 relies on the opening and closing motion of its peptidase domain (PD). In this study, we investigated the possibility of allosterically controlling the ACE2 PD functional dynamics. After confirming that ACE2 PD binding site opening-closing motion is dominant in characterizing its conformational landscape, we observed that few mutations in the viral receptor binding domain fragments were able to impart different effects on the binding site opening of ACE2 PD. This showed that binding to the solvent exposed area of ACE2 PD can effectively alter the conformational profile of the protein, and thus likely its catalytic function. Using a targeted machine learning model and relative entropy-based statistical analysis, we proposed the mechanism for the allosteric perturbation that regulates the ACE2 PD binding site dynamics at atomistic level. The key residues and the source of the allosteric regulation of ACE PD dynamics are also presented.
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Affiliation(s)
- Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Nischal Karki
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Niraj Verma
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Elfi Kraka
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Brian D Zoltowski
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
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16
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Huang HY, Liao HY, Chen X, Wang SW, Cheng CW, Shahed-Al-Mahmud M, Liu YM, Mohapatra A, Chen TH, Lo JM, Wu YM, Ma HH, Chang YH, Tsai HY, Chou YC, Hsueh YP, Tsai CY, Huang PY, Chang SY, Chao TL, Kao HC, Tsai YM, Chen YH, Wu CY, Jan JT, Cheng TJR, Lin KI, Ma C, Wong CH. Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models. Sci Transl Med 2022; 14:eabm0899. [PMID: 35230146 PMCID: PMC9802656 DOI: 10.1126/scitranslmed.abm0899] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key immunogen, the viral surface spike (S) protein is frequently mutated, and conserved epitopes are shielded by glycans. Here, we revealed that S protein glycosylation has site-differential effects on viral infectivity. We found that S protein generated by lung epithelial cells has glycoforms associated with increased infectivity. Compared to the fully glycosylated S protein, immunization of S protein with N-glycans trimmed to the mono-GlcNAc-decorated state (SMG) elicited stronger immune responses and better protection for human angiotensin-converting enzyme 2 (hACE2) transgenic mice against variants of concern (VOCs). In addition, a broadly neutralizing monoclonal antibody was identified from SMG-immunized mice that could neutralize wild-type SARS-CoV-2 and VOCs with subpicomolar potency. Together, these results demonstrate that removal of glycan shields to better expose the conserved sequences has the potential to be an effective and simple approach for developing a broadly protective SARS-CoV-2 vaccine.
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Affiliation(s)
- Han-Yi Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,GIP-TRIAD Master’s Program in Agro-Biomedical Science, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Hsin-Yu Liao
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Szu-Wen Wang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Wei Cheng
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Yo-Min Liu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Ting-Hua Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jennifer M. Lo
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Min Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsiu-Hua Ma
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsuan Chang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Ho-Yang Tsai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Yen Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Pau-Yi Huang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei 100233, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Han-Chieh Kao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Ya-Min Tsai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Yen-Hui Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Corresponding author. (C.M.); (K.-I.L.); . (C.-H.W.)
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Corresponding author. (C.M.); (K.-I.L.); . (C.-H.W.)
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA.,Corresponding author. (C.M.); (K.-I.L.); . (C.-H.W.)
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17
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Deng J, Cui Q. Electronic Polarization Is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants. J Am Chem Soc 2022; 144:4594-4610. [PMID: 35239338 PMCID: PMC9616648 DOI: 10.1021/jacs.2c00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Buried charged residues play important roles in the modulation of protein stabilities and conformational dynamics and make crucial contributions to protein functions. Considering the generally nonpolar nature of protein interior, a key question concerns the contribution of electronic polarization to the stabilization and properties of buried charges. We answer this question by conducting free energy simulations using the latest polarizable CHARMM force field based on Drude oscillators for a series of Staphylococcal nuclease mutants that involve a buried Glu-Lys pair in different titration states and orientations. While a nonpolarizable model suggests that the ionized form of the buried Glu-Lys pair is more than 40 kcal/mol less stable than the charge-neutral form, the two titration states are comparable in stability when electronic polarization is included explicitly, a result better reconcilable with available experimental data. Analysis of free energy components suggests that additional stabilization of the ionized Glu-Lys pair has contributions from both the enhanced salt-bridge strength and stronger interaction between the ion-pair and surrounding protein residues and penetrated water. Despite the stronger direct interaction between Glu and Lys, the ion-pair exhibits considerably larger and faster structural fluctuations when polarization is included, due to compensation of interactions in the cavity. Collectively, observations from this work provide compelling evidence that electronic polarization is essential to the stability, hydration, dynamics, and therefore function of buried charges in proteins. Therefore, our study advocates for the explicit consideration of electronic polarization for mechanistic and engineering studies that implicate buried charged residues, such as enzymes and ion transporters.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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18
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Wu CY, Cheng CW, Kung CC, Liao KS, Jan JT, Ma C, Wong CH. Glycosite-deleted mRNA of SARS-CoV-2 spike protein as a broad-spectrum vaccine. Proc Natl Acad Sci U S A 2022; 119:e2119995119. [PMID: 35149556 PMCID: PMC8892489 DOI: 10.1073/pnas.2119995119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
Development of the messenger RNA (mRNA) vaccine has emerged as an effective and speedy strategy to control the spread of new pathogens. After vaccination, the mRNA is translated into the real protein vaccine, and there is no need to manufacture the protein in vitro. However, the fate of mRNA and its posttranslational modification inside the cell may affect immune response. Here, we showed that the mRNA vaccine of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with deletion of glycosites in the receptor-binding domain (RBD) or especially the subunit 2 (S2) domain to expose more conserved epitopes elicited stronger antibody and CD8+ T cell responses with broader protection against the alpha, beta, gamma, delta, and omicron variants, compared to the unmodified mRNA. Immunization of such mRNA resulted in accumulation of misfolded spike protein in the endoplasmic reticulum, causing the up-regulation of BiP/GRP78, XBP1, and p-eIF2α to induce cell apoptosis and strong CD8+ T cell response. In addition, dendritic cells (DCs) incubated with S2-glysosite deleted mRNA vaccine increased class I major histocompatibility complex (MHC I) expression. This study provides a direction for the development of broad-spectrum mRNA vaccines which may not be achieved with the use of expressed proteins as antigens.
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Affiliation(s)
- Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Wei Cheng
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
- The Master Program of AI Application in Health Industry, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan
| | - Chih-Chuan Kung
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Kuo-Shiang Liao
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan;
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
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19
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Kulkarni AM, Parate S, Lee G, Kim Y, Jung TS, Lee KW, Ha MW. Computational Simulations Highlight the IL2Rα Binding Potential of Polyphenol Stilbenes from Fenugreek. Molecules 2022; 27:molecules27041215. [PMID: 35209009 PMCID: PMC8880457 DOI: 10.3390/molecules27041215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
Widely used in global households, fenugreek is well known for its culinary and medicinal uses. The various reported medicinal properties of fenugreek are by virtue of the different natural phytochemicals present in it. Regarded as a promising target, interleukin 2 receptor subunit alpha (IL2Rα) has been shown to influence immune responses. In the present research, using in silico techniques, we have demonstrated the potential IL2Rα binding properties of three polyphenol stilbenes (desoxyrhaponticin, rhaponticin, rhapontigenin) from fenugreek. As the first step, molecular docking was performed to assess the binding potential of the fenugreek phytochemicals with IL2Rα. All three phytochemicals demonstrated interactions with active site residues. To confirm the reliability of our molecular docking results, 100 ns molecular dynamics simulations studies were undertaken. As discerned by the RMSD and RMSF analyses, IL2Rα in complex with the desoxyrhaponticin, rhaponticin, and rhapontigenin indicated stability. The RMSD analysis of the phytochemicals alone also demonstrated no significant structural changes. Based on the stable molecular interactions and comparatively slightly better MM/PBSA binding free energy, rhaponticin seems promising. Additionally, ADMET analysis performed for the stilbenes indicated that all of them obey the ADMET rules. Our computational study thus supports further in vitro IL2Rα binding studies on these stilbenes, especially rhaponticin.
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Affiliation(s)
- Apoorva M. Kulkarni
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
| | - Shraddha Parate
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Gihwan Lee
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Yongseong Kim
- School of Cosmetics and Food Development, Kyungnam University, Masan 631-701, Korea;
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Research Institute of Natural Science, College of Veterinary Medicine, Gyeongsang National University, 501-201, 501 Jinju-daero, Jinju-si 52828, Gyeongsangnam-do, Korea;
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea;
- Correspondence: (K.W.L.); (M.W.H.)
| | - Min Woo Ha
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Jeju-do, Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Jeju-do, Korea
- Correspondence: (K.W.L.); (M.W.H.)
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20
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El Hassab M, Hemeda L, Elsayed Z, Al-Rashood S, Amin M, Abdel-Azizf H, Eldehna W. Computational prediction of the potential target of SARS-CoV-2 inhibitor plitidepsin via molecular docking, dynamic simulations and MM-PBSA calculations. Chem Biodivers 2021; 19:e202100719. [PMID: 34813168 PMCID: PMC9011487 DOI: 10.1002/cbdv.202100719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/22/2021] [Indexed: 11/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication depends on the interaction between the viral proteins and the human translation machinery. The cytotoxic peptide plitidepsin was found to inhibit CoV-2 up to 90% at a concentration of 0.88 nM. In vitro studies suggest that this activity may be attributed to the inhibition of the eukaryotic translation elongation factor 1A (eEF1A). However, recent reports raised the potential for other cellular targets which plitidepsin may use to exert its potent antiviral activity. The lack of data about these potential targets represents a major limitation for its structural optimization. This work describes the use of a molecular modeling approach to rationalize the in vitro antiviral activity of plitidepsin and to identify potential cellular targets. The developed protocol involves an initial molecular docking step followed by molecular dynamics and binding free energy calculations. The results reveal the potential for plitidepsin to bind to the active site of the key enzyme SARS-CoV-2 RdRp. The results also highlight the importance of van der Waals interactions for proper binding with the enzyme. We believe that the results presented in this study could provide the grounds for the optimization of plitidepsin analogues as SARS-CoV-2 inhibitors.
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Affiliation(s)
- Mahmoud El Hassab
- King Salman International University, Medicinal chemistry, Ras sudr, Egypt, 35566, Ras sudr, EGYPT
| | - Loah Hemeda
- Beni Suef University Faculty of Pharmacy, medicinal chemistry, Beni-Suef, Beni-Suef, EGYPT
| | - Zainab Elsayed
- Kafrelsheikh University, Pharmaceutical chemistry, Kafrelsheikh, Kafrelsheikh, EGYPT
| | - Sara Al-Rashood
- King Saud University College of Pharmacy, pharmaceutical chemistry, Riyad, Riyad, SAUDI ARABIA
| | - Mohammed Amin
- South Metropolitan Health Service, south metropolitan health service, Murdoch, Murdoch, AUSTRALIA
| | - Hatem Abdel-Azizf
- National Research Center Inc, Applied organic chemistry, Dokki, Dokki, EGYPT
| | - Wagdy Eldehna
- Kafrelsheikh University, pharmaceutical chemistry, Faculty of pharmacy, Kafrelsheikh University, 33516, Kafrelsheikh, EGYPT
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21
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Ghosh S, Pandit G, Debnath S, Chatterjee S, Satpati P. Effect of monovalent salt concentration and peptide secondary structure in peptide-micelle binding. RSC Adv 2021; 11:36836-36849. [PMID: 35494385 PMCID: PMC9043568 DOI: 10.1039/d1ra06772a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Recently, we reported a cationic 14 residue peptide LL-14 (LKWLKKLLKWLKKL) with salt-sensitive broad-spectrum antimicrobial potency. However, the mechanism of its salt (NaCl) sensitivity remained unclear. In this study, we have reported computational (∼14.2 μs of MD) and experimental (CD, fluorescence) investigations to examine the salt-sensitivity and the role of peptide secondary structure on LL-14 binding to simple membrane mimetic (SDS, DPC) systems. LL-14 was shown to adopt a random coil (Pc) conformation in water and α-helical conformation (Ph) in the peptide:SDS micelle complex, accompanied by tryptophan burial, using both simulations and experiments. Simulations successfully deconvoluted the LL-14:micelle binding event in terms of secondary structure (random coil Pcversus helix Ph) and gave atomic insight into the initial and final LL-14:SDS complexes. Electrostatics drove the N-terminus (L1 and K2) of LL-14 (Pc or Ph) to bind the SDS micellar surface, initiating complex formation. LL-14 in amphipathic Ph conformation bound faster and buried deeper into the SDS micelle relative to Pc. Increasing NaCl concentration incrementally delayed LL-14:micelle binding by shielding the overall charges of the interacting partners. LL-14 binding to the SDS micelle was significantly faster relative to that of the zwitterionic DPC micelle due to electrostatic reasons. Cationic α-helical amphipathic peptides (with positively charged N-terminus) with low salt-ion concentration seemed to be ideal for faster SDS binding. We report computational (∼14.2 μs of MD) and experimental (CD, fluorescence) investigations to examine the salt-sensitivity and the role of the peptide secondary structure on LL-14 binding to simple membrane mimetic systems.![]()
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2582249 +91-361-2583205
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Swapna Debnath
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2582249 +91-361-2583205
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22
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Yu F, Wang Y, Teng Y, Yang S, He Y, Zhang Z, Yang H, Ding CF, Zhou P. Interaction and Inhibition of a Ganoderma lucidum Proteoglycan on PTP1B Activity for Anti-diabetes. ACS OMEGA 2021; 6:29804-29813. [PMID: 34778653 PMCID: PMC8582033 DOI: 10.1021/acsomega.1c04244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/18/2021] [Indexed: 05/05/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin and an effective target for the treatment of type 2 diabetes (T2D). A natural hyperbranched proteoglycan extracted from Ganoderma lucidum, namely, Fudan-Yueyang G. Lucidum (FYGL), was demonstrated capable of inhibiting the activity of PTP1B. Here, to identify the effective active components of FYGL, three different components, the polysaccharide FYGL-1, proteoglycans FYGL-2, and FYGL-3, were isolated from FYGL, and then, the protein moiety of FYGL-3 was further separated, namely, FYGL-3-P. Their abilities to enhance the glucose uptake in cells and inhibit the activity of PTP1B were compared. The inhibitory mechanisms were systematically explored by spectroscopic methods and MD simulations. The results showed that FYGL-3 and FYGL-3-P significantly enhanced the insulin-provoked glucose uptake in insulin-resistant HepG2 cells, detected by the glucose oxidase method. Also, the FYGL-3-P protein moiety in FYGL played an essential role in inhibiting the activity of PTP1B. A strong, enthalpy-driven, and multitargeted interaction by electrostatic forces between PTP1B and FYGL-3-P dramatically inhibited the catalytic activity of PTP1B. These results provided deep insights into the molecular mechanisms of FYGL inhibiting the activity of PTP1B and structurally helped researchers seek natural PTP1B inhibitors.
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Affiliation(s)
- Fanzhen Yu
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yingxin Wang
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yilong Teng
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Shutong Yang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Yanming He
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Zeng Zhang
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Hongjie Yang
- Yueyang
Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, P. R. China
| | - Chuan-Fan Ding
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Zhejiang
Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular
Analysis, Institute of Mass Spectrometry, School of Material Science
and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Ping Zhou
- State
Key Laboratory of Molecular Engineering of Polymers, Department of
Macromolecular Science, Fudan University, Shanghai 200433, China
- . Phone/Fax: (+86)021-31244038
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23
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Wang X, Wang D, Wang Q, Huang W, Dongye M, Zhang X, Lin D, Lin Z, Li J, Hu W, Li X, Lin X, Zhong Q, Chen W, Lin H. Broadening the Mutation Spectrum in GJA8 and CHMP4B: Novel Missense Variants and the Associated Phenotypes in Six Chinese Han Congenital Cataracts Families. Front Med (Lausanne) 2021; 8:713284. [PMID: 34722561 PMCID: PMC8554029 DOI: 10.3389/fmed.2021.713284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose: To broaden the mutation and phenotype spectrum of the GJA8 and CHMP4B genes and to reveal genotype-phenotype correlations in a cohort of Chinese patients with congenital cataracts (CCs). Methods: Six Chinese Han families with CCs inherited in an autosomal dominant (AD) pattern were recruited for this study. All patients underwent full ocular examinations. Genomic DNA was extracted from the leukocytes of peripheral blood collected from all available patients and their unaffected family members. Whole-exome sequencing (WES) was performed on all probands and at least one of their parents. Candidate variants were further confirmed by Sanger sequencing. Bioinformatic analysis with several computational predictive programs was performed to assess the impacts of the candidate variants on the structure and function of the proteins. Results: Four heterozygous candidate variants in three different genes (CRYBB2, GJA8, and CHMP4B) were identified in affected individuals from the six families, including two novel missense variants (GJA8: c.64G > C/p. G22R, and CHMP4B: c.587C > G/p. S196C), one missense mutation (CRYBB2: c.562C > T/p. R188C), and one small deletion (GJA8: c.426_440delGCTGGAGGGGACCCT/p.143_147delLEGTL). The three missense mutations were predicted as deleterious in all four computational prediction programs. In the homologous model, the GJA8: p.143_147delLEGTL mutation showed a sequence deletion of five amino acids at the cytoplasmic loop of the Cx50 protein, close to the third transmembrane domain. Patients carrying mutations in the same gene showed similar cataract phenotypes at a young age, including total cataracts, Y-sutural with fetal nuclear cataracts, and subcapsular cataracts. Conclusion: This study further expands the mutation spectrum and genotype-phenotype correlation of CRYBB2, GJA8, and CHMP4B underlying CCs. This study sheds light on the importance of comparing congenital cataract phenotypes in patients at the same age stage. It offers clues for the pathogenesis of CCs and allows for an early prenatal diagnosis for families carrying these genetic variants.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Dongni Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Weiming Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Meimei Dongye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xulin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Duoru Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhuoling Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Weiling Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiuping Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Weirong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
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24
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Pablos I, Machado Y, de Jesus HCR, Mohamud Y, Kappelhoff R, Lindskog C, Vlok M, Bell PA, Butler GS, Grin PM, Cao QT, Nguyen JP, Solis N, Abbina S, Rut W, Vederas JC, Szekely L, Szakos A, Drag M, Kizhakkedathu JN, Mossman K, Hirota JA, Jan E, Luo H, Banerjee A, Overall CM. Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL pro substrate degradome. Cell Rep 2021; 37:109892. [PMID: 34672947 PMCID: PMC8501228 DOI: 10.1016/j.celrep.2021.109892] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022] Open
Abstract
The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.
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Affiliation(s)
- Isabel Pablos
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hugo C Ramos de Jesus
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter M Grin
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Quynh T Cao
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Jenny P Nguyen
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Nestor Solis
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Srinivas Abbina
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Laszlo Szekely
- Department of Pathology and Cytology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Attila Szakos
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratories, 141 86 Stockholm, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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25
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The Molecular Basis for Escherichia coli O157:H7 Phage FAHEc1 Endolysin Function and Protein Engineering to Increase Thermal Stability. Viruses 2021; 13:v13061101. [PMID: 34207694 PMCID: PMC8228626 DOI: 10.3390/v13061101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 02/02/2023] Open
Abstract
Bacteriophage-encoded endolysins have been identified as antibacterial candidates. However, the development of endolysins as mainstream antibacterial agents first requires a comprehensive biochemical understanding. This study defines the atomic structure and enzymatic function of Escherichia coli O157:H7 phage FAHEc1 endolysin, LysF1. Bioinformatic analysis suggests this endolysin belongs to the T4 Lysozyme (T4L)-like family of proteins and contains a highly conserved catalytic triad. We then solved the structure of LysF1 with x-ray crystallography to 1.71 Å. LysF1 was confirmed to exist as a monomer in solution by sedimentation velocity experiments. The protein architecture of LysF1 is conserved between T4L and related endolysins. Comparative analysis with related endolysins shows that the spatial orientation of the catalytic triad is conserved, suggesting the catalytic mechanism of peptidoglycan degradation is the same as that of T4L. Differences in the sequence illustrate the role coevolution may have in the evolution of this fold. We also demonstrate that by mutating a single residue within the hydrophobic core, the thermal stability of LysF1 can be increased by 9.4 °C without compromising enzymatic activity. Overall, the characterization of LysF1 provides further insight into the T4L-like class of endolysins. Our study will help advance the development of related endolysins as antibacterial agents, as rational engineering will rely on understanding mutable positions within this protein fold.
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26
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Prathiviraj R, Chellapandi P. Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage. Protein J 2020; 39:33-45. [PMID: 31760575 DOI: 10.1007/s10930-019-09876-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The pupylation pathway marks proteins for prokaryotic ubiquitin-like protein (Pup)-proteasomal degradation and survival strategy of mycobacteria inside of the host macrophages. Deamidase of Pup (Dop) plays a central role in the pupylation pathway. It is still a matter of investigation to know the function of Dop in virulence of mycobacterial lineage. Hence, the present study was intended to describe the sequence-structure-function-virulence link of Dop for understanding the molecular virulence mechanism of Mycobacterium tuberculosis H37Rv (Mtb). Phylogenetic analysis of this study indicated that Dop has extensively diverged across the proteasome-harboring bacteria. The functional part of Dop was converged across the pathogenic mycobacterial lineage. The genome-wide analysis pointed out that the pupylation gene locus was identical to each other, but its genome neighborhood differed from species to species. Molecular modeling and dynamic studies proved that the predicted structure of Mtb Dop was energetically stable and low conformational freedom. Moreover, evolutionary constraints in Mtb Dop were intensively analyzed for inferring its sequence-structure-function relationships for the full virulence of Mtb. It indicated that evolutionary optimization was extensively required to stabilize its local structural environment at the side chains of mutable residues. The sequence-structure-function-virulence link of Dop might have retained in Mtb by reordering hydrophobic and hydrogen bonding patterns in the local structural environment. Thus, the results of our study provide a quest to understand the molecular virulence and pathogenesis mechanisms of Mtb during the infection process.
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Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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27
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Besse A, Brezavar D, Hanson J, Larson A, Bonnen PE. LONP1 de novo dominant mutation causes mitochondrial encephalopathy with loss of LONP1 chaperone activity and excessive LONP1 proteolytic activity. Mitochondrion 2020; 51:68-78. [PMID: 31923470 DOI: 10.1016/j.mito.2020.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/16/2019] [Accepted: 01/03/2020] [Indexed: 02/04/2023]
Abstract
LONP1 is an ATP-dependent protease and chaperone that plays multiple vital roles in mitochondria. LONP1 is essential for mitochondrial homeostasis due to its role in maintenance of the mitochondrial genome and its central role in regulating mitochondrial processes such as oxidative phosphorylation, mitophagy, and heme biosynthesis. Bi-allelic LONP1 mutations have been reported to cause a constellation of clinical presentations. We report a patient heterozygous for a de novo mutation in LONP1: c.901C>T,p.R301W presenting as a neonate with seizures, encephalopathy, pachygyria and microcephaly. Assays of respiratory chain activity in muscle showed complex II-III function at 8% of control. Functional studies in patient fibroblasts showed a signature of dysfunction that included significant decreases in known proteolytic targets of LONP1 (TFAM, PINK1, phospho-PDH E1α) as well as loss of mitochondrial ribosome subunits MRPL44 and MRPL11 with concomitant decreased activity and level of protein subunits of oxidative phosphorylation complexes I and IV. These results indicate excessive LONP1 proteolytic activity and a loss of LONP1 chaperone activity. Further, we demonstrate that the LONP1 N-terminal domain is involved in hexamer stability of LONP1 and that the ability to make conformational changes is necessary for LONP1 to regulate proper functioning of both its proteolytic and chaperone activities.
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Affiliation(s)
- Arnaud Besse
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Brezavar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jennifer Hanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Austin Larson
- University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, United States
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.
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28
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Zhang H, Kai ELJ, Lu L. Investigating the stability of dengue virus envelope protein dimer using well-tempered metadynamics simulations. Proteins 2019; 88:643-653. [PMID: 31697409 DOI: 10.1002/prot.25844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/24/2019] [Accepted: 11/03/2019] [Indexed: 12/21/2022]
Abstract
We explored the stability of the dengue virus envelope (E) protein dimer since it is widely assumed that the E protein dimer is stabilized by drug ligands or antibodies in an acidic environment, neutralizing the virus's ability to fuse with human cells. During this process, a large conformational change of the E protein dimer is required. We performed Molecular Dynamics simulations to mimic the conformational change and stability of the dimer in neutral and acidic conditions with the well-tempered metadynamics method. Furthermore, as a few neutralizing antibodies discovered from dengue patients were reported, we used the same simulation method to examine the influence of a selected antibody on the dimer stability in both neutral and acidic conditions. We also investigated the antibody's influence on a point-mutated E protein that had been reported to interrupt the protein-antibody interaction and result in more than 95% loss of the antibody's binding ability. Our simulation results are highly consistent with the experimental conclusion that binding of the antibody to the E protein dimer neutralizes the virus, especially in a low pH condition, while the mutation of W101A or N153A significantly reduces the antibody's ability in stabilizing the E protein dimer. We demonstrate that well-tempered metadynamics can be used to accurately explore the antibody's interaction on large protein complexes such as the E protein dimer, and the computational approach in this work is promising in future antibody development.
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Affiliation(s)
- Haiping Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong Province, People's Republic of China
| | - Eric L J Kai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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29
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Murugan A, Prathiviraj R, Mothay D, Chellapandi P. Substrate-imprinted docking of Agrobacterium tumefaciens uronate dehydrogenase for increased substrate selectivity. Int J Biol Macromol 2019; 140:1214-1225. [PMID: 31472210 DOI: 10.1016/j.ijbiomac.2019.08.194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/15/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022]
Abstract
Agrobacterium tumefaciens uronate dehydrogenase (AtuUdh) belongs to the short-chain dehydrogenase superfamily, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. It is apparently required for the production of D-glucaric acid. AtuUdh-catalyzed reaction is reversible with dual substrate-specific activity (D-galacturonic acid and D-glucuronic acid) in nature. In our study, 34 mutants were pre-screened from 155 mutants generated from AtuUdh (wild-type) and selected 10 structurally stable mutants with increased substrate selectivity. The specificity, efficiency, and selectivity of these mutants for different substrates and cofactors were predicted from 121 docked models using a substrate-imprinted docking approach. Q14F, S36L, and S75T mutants have shown a high binding affinity to D-glucuronic acid and its substrate intermediates such as D-glucaro-1,4-lactone and D-glucaro-1,5-lactone. These mutants exhibited a low binding affinity to the substrate and cofactor required for D-galactaric acid. D34S, N112E and S165E mutants found to show a high selectivity of D-galacturonic acid and its substrate intermediates for D-galactaric acid production. Ser75, Ser165, and Arg174 are active residues playing an imperative role in the substrate selectivity and also contributed in the conjecture the mechanism of transition state stabilization catalyzed by AtuUdh mutants. The present approach was used to reveal the substrate binding mechanism of AtuUdh mutants for a better understanding of the structural basis for selectivity and function.
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Affiliation(s)
- A Murugan
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Dipti Mothay
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
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30
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Yrazu FM, Pinamonti G, Clementi C. The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family. J Phys Chem B 2018; 122:11800-11806. [PMID: 30277393 DOI: 10.1021/acs.jpcb.8b08676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The trio of protein segment repeats called spectrins diverges by more than 2 orders of magnitude in their folding and unfolding rates, despite having very similar stabilities and almost coincidental topologies. Experimental studies revealed that the mutation of five particular residues dramatically alters the kinetic rates in the slow folders, making them similar to the rates of the fast folder. This is considered to be an exceptional behavior which seems in principle to challenge the current understanding of the protein folding process. In this work, we analyze this scenario, using a simplified computational model, combined with state-of-the-art kinetic analysis techniques. Our model faithfully separates the kinetics of the fast and slow folders and captures the effect of the five mutations. We show that the inclusion of electrostatics in the model is necessary to explain the experimental findings.
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Affiliation(s)
- Fernando Miguel Yrazu
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Giovanni Pinamonti
- Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany
| | - Cecilia Clementi
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States.,Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany.,Center for Theoretical Biological Physics and Department of Chemistry , Rice University , Houston , Texas 77005 , United States
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31
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Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Arch Biochem Biophys 2018; 653:97-106. [PMID: 30018019 DOI: 10.1016/j.abb.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 06/30/2018] [Accepted: 07/05/2018] [Indexed: 11/22/2022]
Abstract
Glu-267 is highly conserved in alcohol dehydrogenases and buried as a negatively-charged residue in a loop of the NAD coenzyme binding domain. Glu-267 might have a structural role and contribute to a rate-promoting vibration that facilitates catalysis. Substitutions of Glu-267 with histidine or asparagine residues increase the dissociation constants for the coenzymes (NAD+ by ∼40-fold, NADH by ∼200-fold) and significantly decrease catalytic efficiencies by 16-1200-fold various substrates and substituted enzymes. The turnover numbers modestly change with the substitutions, but hydride transfer is at least partially rate-limiting for turnover for alcohol oxidation. X-ray structures of the E267H and E267 N enzymes are similar to the apoenzyme (open) conformation of the wild-type enzyme, and the substitutions are accommodated by local changes in the structure. Surprisingly, the E267H and E267 N enzymes have endogenous (from the expression in E. coli) 3'-dephosphocoenzyme A bound in the active site with the ADP moiety in the NAD binding site and the pantethiene sulfhydryl bound to the catalytic zinc. The kinetics and crystallography show that the substitutions of Glu-267 hinder the conformational change, which occurs when wild-type enzyme binds coenzymes, and affect productive binding of substrates.
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32
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Kiewiet MBG, Dekkers R, Ulfman LH, Groeneveld A, de Vos P, Faas MM. Immunomodulating protein aggregates in soy and whey hydrolysates and their resistance to digestion in an in vitro infant gastrointestinal model: new insights in the mechanism of immunomodulatory hydrolysates. Food Funct 2018; 9:604-613. [PMID: 29271442 DOI: 10.1039/c7fo01537b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hydrolysates, which are used in hypoallergenic infant formulas, have been found to possess immune modulating effects. For an optimal utilization of hydrolysates, the working mechanisms and responsible proteins underlying the effects should be elucidated. In this study, the immunomodulating activity of whey and soy hydrolysates was studied by quantifying TLR activation and assessing cytokine production in hydrolysate stimulated dendritic cells. The responsible protein fraction was identified and characterized by gel electrophoresis. The immune effects under gastrointestinal conditions were studied by digesting the hydrolysates in an in vitro infant digestion model, after which the digests were analyzed. In both soy and whey hydrolysates, TLR activation and cytokine production in dendritic cells were induced by a fraction containing protein aggregates larger than 1000 kDa, which were formed by electrostatic interactions and disulfide bonds. Only soy aggregates remained intact during duodenal digestion, and maintained the TLR activating capacity. Soy and whey protein aggregates larger than 1000 kDa possess immunomodulatory properties, but only soy aggregates remain under intestinal digestion conditions. This knowledge is important for a better understanding of the effects of hydrolysates.
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Affiliation(s)
- Mensiena B G Kiewiet
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands.
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33
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Affiliation(s)
- Shridhar K. Sathe
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Valerie D. Zaffran
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Sahil Gupta
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Tengfei Li
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
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34
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Carmali S, Murata H, Amemiya E, Matyjaszewski K, Russell AJ. Tertiary Structure-Based Prediction of How ATRP Initiators React with Proteins. ACS Biomater Sci Eng 2017; 3:2086-2097. [DOI: 10.1021/acsbiomaterials.7b00281] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sheiliza Carmali
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Hironobu Murata
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Erika Amemiya
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Alan J. Russell
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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35
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Medvedev KE, Kolchanov NA, Afonnikov DA. High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations. J Biomol Struct Dyn 2017; 36:68-82. [DOI: 10.1080/07391102.2016.1268070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill E. Medvedev
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolay A. Kolchanov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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36
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Differential protein structural disturbances and suppression of assembly partners produced by nonsense GABRG2 epilepsy mutations: implications for disease phenotypic heterogeneity. Sci Rep 2016; 6:35294. [PMID: 27762395 PMCID: PMC5071880 DOI: 10.1038/srep35294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/14/2016] [Indexed: 12/01/2022] Open
Abstract
Mutations in GABAA receptor subunit genes are frequently associated with epilepsy, and nonsense mutations in GABRG2 are associated with several epilepsy syndromes including childhood absence epilepsy, generalized tonic clonic seizures and the epileptic encephalopathy, Dravet syndrome. The molecular basis for the phenotypic heterogeneity of mutations is unclear. Here we focused on three nonsense mutations in GABRG2 (GABRG2(R136*), GABRG2(Q390*) and GABRG2(W429*)) associated with epilepsies of different severities. Structural modeling and structure-based analysis indicated that the surface of the wild-type γ2 subunit was naturally hydrophobic, which is suitable to be buried in the cell membrane. Different mutant γ2 subunits had different stabilities and different interactions with their wild-type subunit binding partners because they adopted different conformations and had different surface hydrophobicities and different tendency to dimerize. We utilized flow cytometry and biochemical approaches in combination with lifted whole cell patch-clamp recordings. We demonstrated that the truncated subunits had no to minimal surface expression and unchanged or reduced surface expression of wild-type partnering subunits. The amplitudes of GABA-evoked currents from the mutant α1β2γ2(R136*), α1β2γ2(Q390*) and α1β2γ2(W429*) receptors were reduced compared to the currents from α1β2γ2 receptors but with differentially reduced levels. This thus suggests differential protein structure disturbances are correlated with disease severity.
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37
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Structural constraints-based evaluation of immunogenic avirulent toxins from Clostridium botulinum C2 and C3 toxins as subunit vaccines. INFECTION GENETICS AND EVOLUTION 2016; 44:17-27. [PMID: 27320793 DOI: 10.1016/j.meegid.2016.06.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 05/26/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 and C3 toxins in addition to botulinum neurotoxins in avian and mammalian cells. C2 and C3 toxins are members of bacterial ADP-ribosyltransferase superfamily, which modify the eukaryotic cell surface proteins by ADP-ribosylation reaction. Herein, the mutant proteins with lack of catalytic and pore forming function derived from C2 (C2I and C2II) and C3 toxins were computationally evaluated to understand their structure-function integrity. We have chosen many structural constraints including local structural environment, folding process, backbone conformation, conformational dynamic sub-space, NAD-binding specificity and antigenic determinants for screening of suitable avirulent toxins. A total of 20 avirulent mutants were identified out of 23 mutants, which were experimentally produced by site-directed mutagenesis. No changes in secondary structural elements in particular to α-helices and β-sheets and also in fold rate of all-β classes. Structural stability was maintained by reordered hydrophobic and hydrogen bonding patterns. Molecular dynamic studies suggested that coupled mutations may restrain the binding affinity to NAD(+) or protein substrate upon structural destabilization. Avirulent toxins of this study have stable energetic backbone conformation with a common blue print of folding process. Molecular docking studies revealed that avirulent mutants formed more favorable hydrogen bonding with the side-chain of amino acids near to conserved NAD-binding core, despite of restraining NAD-binding specificity. Thus, structural constraints in the avirulent toxins would determine their immunogenic nature for the prioritization of protein-based subunit vaccine/immunogens to avian and veterinary animals infected with C. botulinum.
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38
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McCauliff LA, Xu Z, Li R, Kodukula S, Ko DC, Scott MP, Kahn PC, Storch J. Multiple Surface Regions on the Niemann-Pick C2 Protein Facilitate Intracellular Cholesterol Transport. J Biol Chem 2015; 290:27321-27331. [PMID: 26296895 DOI: 10.1074/jbc.m115.667469] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Indexed: 01/07/2023] Open
Abstract
The cholesterol storage disorder Niemann-Pick type C (NPC) disease is caused by defects in either of two late endosomal/lysosomal proteins, NPC1 and NPC2. NPC2 is a 16-kDa soluble protein that binds cholesterol in a 1:1 stoichiometry and can transfer cholesterol between membranes by a mechanism that involves protein-membrane interactions. To examine the structural basis of NPC2 function in cholesterol trafficking, a series of point mutations were generated across the surface of the protein. Several NPC2 mutants exhibited deficient sterol transport properties in a set of fluorescence-based assays. Notably, these mutants were also unable to promote egress of accumulated intracellular cholesterol from npc2(-/-) fibroblasts. The mutations mapped to several regions on the protein surface, suggesting that NPC2 can bind to more than one membrane simultaneously. Indeed, we have previously demonstrated that WT NPC2 promotes vesicle-vesicle interactions. These interactions were abrogated, however, by mutations causing defective sterol transfer properties. Molecular modeling shows that NPC2 is highly plastic, with several intense positively charged regions across the surface that could interact favorably with negatively charged membrane phospholipids. The point mutations generated in this study caused changes in NPC2 surface charge distribution with minimal conformational changes. The plasticity, coupled with membrane flexibility, probably allows for multiple cholesterol transfer routes. Thus, we hypothesize that, in part, NPC2 rapidly traffics cholesterol between closely appositioned membranes within the multilamellar interior of late endosomal/lysosomal proteins, ultimately effecting cholesterol egress from this compartment.
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Affiliation(s)
- Leslie A McCauliff
- Department of Nutritional Sciences and Rutgers Center for Lipid Research and
| | - Zhi Xu
- Department of Nutritional Sciences and Rutgers Center for Lipid Research and
| | - Ran Li
- Department of Nutritional Sciences and Rutgers Center for Lipid Research and
| | - Sarala Kodukula
- Department of Nutritional Sciences and Rutgers Center for Lipid Research and
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Matthew P Scott
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Peter C Kahn
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901
| | - Judith Storch
- Department of Nutritional Sciences and Rutgers Center for Lipid Research and.
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39
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Wu H, Zeng H, Lam R, Tempel W, Kerr ID, Min J. Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome. Acta Crystallogr F Struct Biol Commun 2015; 71:981-5. [PMID: 26249686 PMCID: PMC4528928 DOI: 10.1107/s2053230x15010183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/26/2015] [Indexed: 02/25/2023] Open
Abstract
Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson-Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.
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Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Iain D. Kerr
- Myriad Genetic Laboratories Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada
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40
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Wang Y, Wang J, Yao L. Computational Study of Peptide Plane Stacking with Polar and Ionizable Amino Acid Side Chains. J Phys Chem A 2015; 119:3471-8. [DOI: 10.1021/acs.jpca.5b00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yefei Wang
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
| | - Jia Wang
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
| | - Lishan Yao
- Laboratory of Biofuels, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao 266061, China
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41
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He C, Chen J, An L, Wang Y, Shu Z, Yao L. Carboxyl-peptide plane stacking is important for stabilization of buried E305 of Trichoderma reesei Cel5A. J Chem Inf Model 2015; 55:104-13. [PMID: 25569819 DOI: 10.1021/ci500610m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonds or salt bridges are usually formed to stabilize the buried ionizable residues. However, such interactions do not exist for two buried residues D271 and E305 of Trichoderma reesei Cel5A, an endoglucanase. Mutating D271 to alanine or leucine improves the enzyme thermostability quantified by the temperature T50 due to the elimination of the desolvation penalty of the aspartic acid. However, the same mutations for E305 decrease the enzyme thermostability. Free energy calculations based on the molecular dynamics simulation predict the thermostability of D271A, D271L, and E305A (compared to WT) in line with the experimental observation but overestimate the thermostability of E305L. Quantum mechanical calculations suggest that the carboxyl-peptide plane stacking interactions occurring to E305 but not D271 are important for the carboxyl group stabilization. For the protonated carboxyl group, the interaction energy can be as much as about -4 kcal/mol for parallel stacking and about -7 kcal/mol for T-shaped stacking. For the deprotonated carboxyl group, the largest interaction energies for parallel stacking and T-shaped stacking are comparable, about -7 kcal/mol. The solvation effect generally weakens the interaction, especially for the charged system. A search of the carboxyl-peptide plane stacking in the PDB databank indicates that parallel stacking but not T-shaped stacking is quite common, and the most probable distance between the two stacking fragments is close to the value predicted by the QM calculations. This work highlights the potential role of carboxyl amide π-π stacking in the stabilization of aspartic acid and glutamic acid in proteins.
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Affiliation(s)
- Chunyan He
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266061, China
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Abstract
The molecular mechanisms underlying pressure-induced protein denaturation can be analyzed based on the pressure-dependent differences in the apparent volume occupied by amino acids inside the protein and when exposed to water in an unfolded conformation. This chapter presents a volumetric analysis of the peptide group and the 20 naturally occurring amino acid side chains in the interior of the native state, the micelle-like interior of the pressure-induced denatured state, and in the unfolded conformation modeled by low-molecular analogs of proteins. The transfer of a peptide group from the protein interior to water becomes increasingly favorable as pressure increases. This observation classifies solvation of peptide groups as a major driving force in pressure-induced protein denaturation. Polar side chains do not appear to exhibit significant pressure-dependent changes in their preference for the protein interior or solvent. The transfer of nonpolar side chains from the protein interior to water becomes more unfavorable as pressure increases. An inference can be drawn that a sizeable population of nonpolar side chains remains buried inside a solvent-inaccessible core of the pressure-induced denatured state. At elevated pressures this core, owing to the absence of structural constraints, may become packed almost as tightly as the interior of the native state. The presence and partial disappearance of large intraglobular voids is another driving force facilitating pressure-induced protein denaturation. Volumetric data presented here have implications for the kinetics of protein folding and shed light on the nature of the folding transition state ensembles.
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43
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Boersma YL, Newman J, Adams TE, Cowieson N, Krippner G, Bozaoglu K, Peat TS. The structure of vanin 1: a key enzyme linking metabolic disease and inflammation. ACTA ACUST UNITED AC 2014; 70:3320-9. [PMID: 25478849 DOI: 10.1107/s1399004714022767] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023]
Abstract
Although part of the coenzyme A pathway, vanin 1 (also known as pantetheinase) sits on the cell surface of many cell types as an ectoenzyme, catalyzing the breakdown of pantetheine to pantothenic acid (vitamin B5) and cysteamine, a strong reducing agent. Vanin 1 was initially discovered as a protein involved in the homing of leukocytes to the thymus. Numerous studies have shown that vanin 1 is involved in inflammation, and more recent studies have shown a key role in metabolic disease. Here, the X-ray crystal structure of human vanin 1 at 2.25 Å resolution is presented, which is the first reported structure from the vanin family, as well as a crystal structure of vanin 1 bound to a specific inhibitor. These structures illuminate how vanin 1 can mediate its biological roles by way of both enzymatic activity and protein-protein interactions. Furthermore, it sheds light on how the enzymatic activity is regulated by a novel allosteric mechanism at a domain interface.
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Affiliation(s)
- Ykelien L Boersma
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Janet Newman
- CSIRO Biosciences Program, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Timothy E Adams
- CSIRO Biosciences Program, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Nathan Cowieson
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Guy Krippner
- Baker IDI, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Kiymet Bozaoglu
- Baker IDI, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Thomas S Peat
- CSIRO Biosciences Program, 343 Royal Parade, Parkville, VIC 3052, Australia
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Kolomytseva M, Ferraroni M, Chernykh A, Golovleva L, Scozzafava A. Structural basis for the substrate specificity and the absence of dehalogenation activity in 2-chloromuconate cycloisomerase from Rhodococcus opacus 1CP. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1541-9. [DOI: 10.1016/j.bbapap.2014.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/09/2014] [Accepted: 04/13/2014] [Indexed: 11/26/2022]
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45
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Nick Pace C, Scholtz JM, Grimsley GR. Forces stabilizing proteins. FEBS Lett 2014; 588:2177-84. [PMID: 24846139 DOI: 10.1016/j.febslet.2014.05.006] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 11/30/2022]
Abstract
The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a -CH2- group on folding contributes 1.1±0.5 kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8 kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.
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Affiliation(s)
- C Nick Pace
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States.
| | - J Martin Scholtz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
| | - Gerald R Grimsley
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
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46
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A coarse-grained protein model in a water-like solvent. Sci Rep 2013; 3:1841. [PMID: 23674146 PMCID: PMC3653448 DOI: 10.1038/srep01841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/29/2013] [Indexed: 02/07/2023] Open
Abstract
Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (“H-P”) model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the “Jagla-philic” monomers to the solvent, while maintaining a “hydrophobic” core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.
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Isom DG, Sridharan V, Baker R, Clement ST, Smalley DM, Dohlman HG. Protons as second messenger regulators of G protein signaling. Mol Cell 2013; 51:531-8. [PMID: 23954348 DOI: 10.1016/j.molcel.2013.07.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/11/2013] [Accepted: 06/26/2013] [Indexed: 12/19/2022]
Abstract
In response to environmental stress, cells often generate pH signals that serve to protect vital cellular components and reprogram gene expression for survival. A major barrier to our understanding of this process has been the identification of signaling proteins that detect changes in intracellular pH. To identify candidate pH sensors, we developed a computer algorithm that searches proteins for networks of proton-binding sidechains. This analysis indicates that Gα subunits, the principal transducers of G protein-coupled receptor (GPCR) signals, are pH sensors. Our structure-based calculations and biophysical investigations reveal that Gα subunits contain networks of pH-sensing sidechains buried between their Ras and helical domains. Further, we show that proton binding induces changes in conformation that promote Gα phosphorylation and suppress receptor-initiated signaling. Together, our computational, biophysical, and cellular analyses reveal an unexpected function for G proteins as mediators of stress-response signaling.
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Affiliation(s)
- Daniel G Isom
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
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Pluhařová E, Marsalek O, Schmidt B, Jungwirth P. Peptide salt bridge stability: from gas phase via microhydration to bulk water simulations. J Chem Phys 2013; 137:185101. [PMID: 23163393 DOI: 10.1063/1.4765052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.
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Affiliation(s)
- Eva Pluhařová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, CZ-16610, Czech Republic.
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Behrens C, Hartmann K, Sunderhaus S, Braun HP, Eubel H. Approximate calculation and experimental derivation of native isoelectric points of membrane protein complexes of Arabidopsis chloroplasts and mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013. [DOI: 10.1016/j.bbamem.2012.11.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chen J, Sawyer N, Regan L. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci 2013; 22:510-5. [PMID: 23389845 DOI: 10.1002/pro.2230] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/27/2013] [Accepted: 01/28/2013] [Indexed: 02/04/2023]
Abstract
Protein-protein interactions play key roles in many cellular processes and their affinities and specificities are finely tuned to the functions they perform. Here, we present a study on the relationship between binding affinity and the size and chemical nature of protein-protein interfaces. Our analysis focuses on heterodimers and includes curated structural and thermodynamic data for 113 complexes. We observe a direct correlation between binding affinity and the amount of surface area buried at the interface. For a given amount of surface area buried, the binding affinity spans four orders of magnitude in terms of the dissociation constant (Kd ). Across the entire dataset, we observe no obvious relationship between binding affinity and the chemical composition of the interface. We also calculate the free energy per unit surface area buried, or "surface energy density," of each heterodimer. For interfacial surface areas between 500 and 2000 Å(2) , the surface energy density decreases as the buried surface area increases. As the buried surface area increases beyond about 2000 Å(2) , the surface energy density levels off to a constant value. We believe that these analyses and data will be useful for researchers with an interest in understanding, designing or inhibiting protein-protein interfaces.
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Affiliation(s)
- Jieming Chen
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
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