1
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Parvez F, Sangpal D, Paithankar H, Amin Z, Chugh J. Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding. eLife 2024; 13:RP94842. [PMID: 39116184 PMCID: PMC11309768 DOI: 10.7554/elife.94842] [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] [Indexed: 08/10/2024] Open
Abstract
Trans-activation response (TAR) RNA-binding protein (TRBP) has emerged as a key player in the RNA interference pathway, wherein it binds to different pre-microRNAs (miRNAs) and small interfering RNAs (siRNAs), each varying in sequence and/or structure. We hypothesize that TRBP displays dynamic adaptability to accommodate heterogeneity in target RNA structures. Thus, it is crucial to ascertain the role of intrinsic and RNA-induced protein dynamics in RNA recognition and binding. We have previously elucidated the role of intrinsic and RNA-induced conformational exchange in the double-stranded RNA-binding domain 1 (dsRBD1) of TRBP in shape-dependent RNA recognition. The current study delves into the intrinsic and RNA-induced conformational dynamics of the TRBP-dsRBD2 and then compares it with the dsRBD1 study carried out previously. Remarkably, the two domains exhibit differential binding affinity to a 12-bp dsRNA owing to the presence of critical residues and structural plasticity. Furthermore, we report that dsRBD2 depicts constrained conformational plasticity when compared to dsRBD1. Although, in the presence of RNA, dsRBD2 undergoes induced conformational exchange within the designated RNA-binding regions and other residues, the amplitude of the motions remains modest when compared to those observed in dsRBD1. We propose a dynamics-driven model of the two tandem domains of TRBP, substantiating their contributions to the versatility of dsRNA recognition and binding.
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Affiliation(s)
- Firdousi Parvez
- Department of Biology, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Devika Sangpal
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune UniversityPuneIndia
| | - Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Zainab Amin
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
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2
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Breimann S, Kamp F, Steiner H, Frishman D. AAontology: An ontology of amino acid scales for interpretable machine learning. J Mol Biol 2024:168717. [PMID: 39053689 DOI: 10.1016/j.jmb.2024.168717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained classification necessary for satisfactory interpretability in many protein prediction problems. To address this issue, we developed AAontology-a two-level classification for 586 amino acid scales (mainly from AAindex) together with an in-depth analysis of their relations-using bag-of-word-based classification, clustering, and manual refinement over multiple iterations. AAontology organizes physicochemical scales into 8 categories and 67 subcategories, enhancing the interpretability of scale-based machine learning methods in protein bioinformatics. Thereby it enables researchers to gain a deeper biological insight. We anticipate that AAontology will be a building block to link amino acid properties with protein function and dysfunctions as well as aid informed decision-making in mutation analysis or protein drug design.
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Affiliation(s)
- Stephan Breimann
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany; Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Frits Kamp
- Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany
| | - Harald Steiner
- Ludwig-Maximilians-University Munich, Biomedical Center, Division of Metabolic Biochemistry, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany.
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3
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Sung AY, Guerra RM, Steenberge LH, Alston CL, Murayama K, Okazaki Y, Shimura M, Prokisch H, Ghezzi D, Torraco A, Carrozzo R, Rötig A, Taylor RW, Keck JL, Pagliarini DJ. Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease. Nat Metab 2024; 6:1128-1142. [PMID: 38720117 DOI: 10.1038/s42255-024-01039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/28/2024] [Indexed: 06/27/2024]
Abstract
Isolated complex I (CI) deficiencies are a major cause of primary mitochondrial disease. A substantial proportion of CI deficiencies are believed to arise from defects in CI assembly factors (CIAFs) that are not part of the CI holoenzyme. The biochemistry of these CIAFs is poorly defined, making their role in CI assembly unclear, and confounding interpretation of potential disease-causing genetic variants. To address these challenges, we devised a deep mutational scanning approach to systematically assess the function of thousands of NDUFAF6 genetic variants. Guided by these data, biochemical analyses and cross-linking mass spectrometry, we discovered that the CIAF NDUFAF6 facilitates incorporation of NDUFS8 into CI and reveal that NDUFS8 overexpression rectifies NDUFAF6 deficiency. Our data further provide experimental support of pathogenicity for seven novel NDUFAF6 variants associated with human pathology and introduce functional evidence for over 5,000 additional variants. Overall, our work defines the molecular function of NDUFAF6 and provides a clinical resource for aiding diagnosis of NDUFAF6-related diseases.
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Affiliation(s)
- Andrew Y Sung
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Laura H Steenberge
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Charlotte L Alston
- Mitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Daniele Ghezzi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Instituto Neurologico Carlo Besta, Milan, Italy
| | - Alessandra Torraco
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Agnès Rötig
- Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Robert W Taylor
- Mitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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4
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Badreldin M, Salas-Ambrosio P, Bourasseau S, Lecommandoux S, Harrisson S, Bonduelle C. Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides. Biomacromolecules 2024; 25:3033-3043. [PMID: 38652289 DOI: 10.1021/acs.biomac.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.
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Affiliation(s)
- Mostafa Badreldin
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Pedro Salas-Ambrosio
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Sylvain Bourasseau
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | | | - Simon Harrisson
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Colin Bonduelle
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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5
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Hu W, Song A, Zheng H. Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2. Nat Commun 2024; 15:3616. [PMID: 38684689 PMCID: PMC11059360 DOI: 10.1038/s41467-024-48028-3] [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: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.
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Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Alex Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US.
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6
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Han W, Wei D, Sun Z, Qu D. Investigating the mechanism of rough phenotype in a naturally attenuated Brucella strain: insights from whole genome sequencing. Front Med (Lausanne) 2024; 11:1363785. [PMID: 38711779 PMCID: PMC11073494 DOI: 10.3389/fmed.2024.1363785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/23/2024] [Indexed: 05/08/2024] Open
Abstract
Objective Brucellosis, a significant zoonotic disease, not only impacts animal health but also profoundly influences the host immune responses through gut microbiome. Our research focuses on whole genome sequencing and comparative genomic analysis of these Brucella strains to understand the mechanisms of their virulence changes that may deepen our comprehension of the host immune dysregulation. Methods The Brucella melitensis strain CMCC55210 and its naturally attenuated variant CMCC55210a were used as models. Biochemical identification tests and in vivo experiments in mice verified the characteristics of the strain. To understand the mechanism of attenuation, we then performed de novo sequencing of these two strains. Results We discovered notable genomic differences between the two strains, with a key single nucleotide polymorphism (SNP) mutation in the manB gene potentially altering lipopolysaccharide (LPS) structure and influencing host immunity to the pathogen. This mutation might contribute to the attenuated strain's altered impact on the host's macrophage immune response, overing insights into the mechanisms of immune dysregulation linked to intracellular survival. Furthermore, we explore that manipulating the Type I restriction-modification system in Brucella can significantly impact its genome stability with the DNA damage response, consequently affecting the host's immune system. Conclusion This study not only contributes to understanding the complex relationship between pathogens, and the immune system but also opens avenues for innovative therapeutic interventions in inflammatory diseases driven by microbial and immune dysregulation.
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Affiliation(s)
- Wendong Han
- BSL-3 Laboratory of Fudan University, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dong Wei
- Division of Tuberculosis Vaccines and Allergen, National Institute for Food and Drug Control, Beijing, China
| | - Zhiping Sun
- BSL-3 Laboratory of Fudan University, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Di Qu
- BSL-3 Laboratory of Fudan University, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, China
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7
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MacPherson DS, Dave D, Kassem S, Doganata S, Zeglis BM, Ulijn RV. Tuning Supramolecular Chirality in Iodinated Amphiphilic Peptides Through Tripeptide Linker Editing. Biomacromolecules 2024; 25:2277-2285. [PMID: 38445833 DOI: 10.1021/acs.biomac.3c01120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Protease-cleavable supramolecular oligopeptide nanofilaments are promising materials for targeted therapeutics and diagnostics. In these systems, single amino acid substitutions can have profound effects on the supramolecular structure and consequent proteolytic degradation, which are critical parameters for their intended applications. Herein, we describe changes to the self-assembly and proteolytic cleavage of iodine containing sequences for future translation into matrix metalloprotease (MMP-9)-activated supramolecular radio-imaging probes. We use a systematic single amino acid exchange in the tripeptide linker region of these peptide amphiphiles to provide insights into the role of each residue in the supramolecular assemblies. These modifications resulted in dramatic changes in the nature of the assembled structures formed, including an unexpected chiral inversion. By using circular dichroism, atomic force microscopy, Fourier transform infrared spectroscopy, and molecular dynamics simulations, we found that the GD loop, a common motif in β-turn elements, induced a reversal of the chiral orientation of the assembled nanofibers. In addition to the impact on peptide packing and chirality, MMP-9-catalyzed hydrolysis was evaluated for the four peptides, with the β-sheet content found to be a stronger determinant of enzymatic hydrolysis than supramolecular chirality. These observations provide fundamental insights into the sequence design in protease cleavable amphiphilic peptides with the potential for radio-labeling and selective biomedical applications.
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Affiliation(s)
- Douglas S MacPherson
- Advanced Science Research Center (ASRC) at The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10028, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Dhwanit Dave
- Advanced Science Research Center (ASRC) at The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10028, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Salma Kassem
- Advanced Science Research Center (ASRC) at The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, New York 10031, United States
| | - Selma Doganata
- Advanced Science Research Center (ASRC) at The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, New York 10031, United States
- Macaulay Honors College, City University of New York, New York, New York 10031, United States
| | - Brian M Zeglis
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10028, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Radiology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at The Graduate Center, City University of New York, 85 Saint Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10028, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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8
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Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
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Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
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9
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Maass D, Boelens P, Bloss C, Claus G, Harter S, Günther D, Pollmann K, Lederer F. Identification of yttrium oxide-specific peptides for future recycling of rare earth elements from electronic scrap. Biotechnol Bioeng 2024; 121:1026-1035. [PMID: 38168837 DOI: 10.1002/bit.28629] [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: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
Yttrium is a heavy rare earth element (REE) that acquires remarkable characteristics when it is in oxide form and doped with other REEs. Owing to these characteristics Y2 O3 can be used in the manufacture of several products. However, a supply deficit of this mineral is expected in the coming years, contributing to its price fluctuation. Thus, developing an efficient, cost-effective, and eco-friendly process to recover Y2 O3 from secondary sources has become necessary. In this study, we used phage surface display to screen peptides with high specificity for Y2 O3 particles. After three rounds of enrichment, a phage expressing the peptide TRTGCHVPRCNTLS (DM39) from the random pVIII phage peptide library Cys4 was found to bind specifically to Y2 O3 , being 531.6-fold more efficient than the wild-type phage. The phage DM39 contains two arginines in the polar side chains, which may have contributed to the interaction between the mineral targets. Immunofluorescence assays identified that the peptide's affinity was strong for Y2 O3 and negligible to LaPO4 :Ce3+ ,Tb3+ . The identification of a peptide with high specificity and affinity for Y2 O3 provides a potentially new strategic approach to recycle this type of material from secondary sources, especially from electronic scrap.
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Affiliation(s)
- Danielle Maass
- Departamento de Ciência e Tecnologia, Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, São Paulo, Brazil
| | | | | | - Gerda Claus
- Department of Biotechnology, Dresden, Germany
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10
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Vanella R, Küng C, Schoepfer AA, Doffini V, Ren J, Nash MA. Understanding activity-stability tradeoffs in biocatalysts by enzyme proximity sequencing. Nat Commun 2024; 15:1807. [PMID: 38418512 PMCID: PMC10902396 DOI: 10.1038/s41467-024-45630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024] Open
Abstract
Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is crucial for applications in industry and biomedicine. However, current enzyme assay technologies are limited by an inability to simultaneously resolve both stability and activity phenotypes and to couple these to gene sequences at large scale. Here we present the development of enzyme proximity sequencing, a deep mutational scanning method that leverages peroxidase-mediated radical labeling with single cell fidelity to dissect the effects of thousands of mutations on stability and catalytic activity of oxidoreductase enzymes in a single experiment. We use enzyme proximity sequencing to analyze how 6399 missense mutations influence folding stability and catalytic activity in a D-amino acid oxidase from Rhodotorula gracilis. The resulting datasets demonstrate activity-based constraints that limit folding stability during natural evolution, and identify hotspots distant from the active site as candidates for mutations that improve catalytic activity without sacrificing stability. Enzyme proximity sequencing can be extended to other enzyme classes and provides valuable insights into biophysical principles governing enzyme structure and function.
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Affiliation(s)
- Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
| | - Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Alexandre A Schoepfer
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- National Center for Competence in Research (NCCR), Catalysis, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Vanni Doffini
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Jin Ren
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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11
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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12
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Pinto ESM, Mangini AT, Novo LCC, Cavatao FG, Krause MJ, Dorn M. Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding. Curr Res Struct Biol 2024; 7:100130. [PMID: 38406590 PMCID: PMC10885555 DOI: 10.1016/j.crstbi.2024.100130] [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: 12/11/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extracted from the bacteria Kaistella jeonii could promiscuously degrade PET. Compared to the well-known PETase from Ideonella sakaiensis, this novel esterase presents a low sequence identity yet has a remarkably similar folding. However, enzymatic assays demonstrated a lower catalytic efficiency. In this work, we employed a strict computational approach to investigate the binding mechanism between the esterase and PET. Understanding the underlying mechanism of binding can shed light on the evolutive mechanism of how enzymes have been evolving to degrade these artificial molecules and help develop rational engineering approaches to improve PETase-like enzymes. Our results indicate that this esterase misses a disulfide bridge, keeping the catalytic residues closer and possibly influencing its catalytic efficiency. Moreover, we describe the structural response to the interaction between enzyme and PET, indicating local and global effects. Our results aid in deepening the knowledge behind the mechanism of biological catalysis of PET degradation and as a base for the engineering of novel PETases.
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Affiliation(s)
- Ederson Sales Moreira Pinto
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Arthur Tonietto Mangini
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Lorenzo Chaves Costa Novo
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Fernando Guimaraes Cavatao
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Mathias J. Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Englerstraße 2, D-76131, Karlsruhe, BW, Germany
| | - Marcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
- Institute of Informatics, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Building 43424, Porto Alegre, RS, Brazil
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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13
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Putri RA, Rohman MS, Swasono RT, Raharjo TJ. A novel synthetic peptide analog enhanced antibacterial activity of the frog-derived skin peptide wuchuanin-A1. J Biomol Struct Dyn 2023:1-11. [PMID: 37968993 DOI: 10.1080/07391102.2023.2281633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
In recent years, there has been a growing focus on the development of novel antibacterial compounds for clinical applications, such as antimicrobial peptide (AMP). Among the developed AMP, wuchuanin-A1, a coil-shaped bioactive peptide derived from Odorrana wuchuanensis frog skin, has been reported to exhibit antibacterial, antifungal, and antioxidant activity, but there are limited studies on its potential as an antibacterial agent. Therefore, this study aims to molecularly modify the sequence of wuchuanin-A1 to enhance its antibacterial properties. The interaction of both the native and analog peptide with bacterial inner membranes was initially assessed using computational methods. Specific amino acid substitutions were then used to enhance the modified peptide's antibacterial efficacy, followed by several preliminary tests to evaluate its activity. This study bridges the gap in exploring the potential of wuchuanin-A1 for antibacterial purposes, providing insights into the design of effective antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Tri Joko Raharjo
- Department of Chemistry, Universitas Gadjah Mada, Bulaksumur, Indonesia
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14
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Aina A, Hsueh SCC, Gibbs E, Peng X, Cashman NR, Plotkin SS. De Novo Design of a β-Helix Tau Protein Scaffold: An Oligomer-Selective Vaccine Immunogen Candidate for Alzheimer's Disease. ACS Chem Neurosci 2023; 14:2603-2617. [PMID: 37458595 DOI: 10.1021/acschemneuro.3c00007] [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] [Indexed: 08/03/2023] Open
Abstract
Tau pathology is associated with many neurodegenerative disorders, including Alzheimer's disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein-misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope 343KLDFK347 was scaffolded by designing a β-helix structure that incorporated multiple instances of the 16-residue tau fragment 339VKSEKLDFKDRVQSKI354. Large-scale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth D showed that the multi-epitope scaffolding approach, employed in designing the β-helix scaffold, was predicted to better discriminate toxic tau oligomers than other "monovalent" strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of the β-helix scaffold, along with a C-terminal stabilizing α-helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead-designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesized β-helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover, the strength of binding of these antibodies to in vitro tau oligomers correlated with the strength of binding to the β-helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.
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Affiliation(s)
- Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ebrima Gibbs
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xubiao Peng
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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15
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Shindo S, Kakizaki S, Sakaki T, Kawasaki Y, Sakuma T, Negishi M, Shizu R. Phosphorylation of nuclear receptors: Novelty and therapeutic implications. Pharmacol Ther 2023:108477. [PMID: 37330113 DOI: 10.1016/j.pharmthera.2023.108477] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/20/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023]
Abstract
Nuclear receptors (NR) collectively regulate several biological functions in various organs. While NRs can be characterized by activation of the transcription of their signature genes, they also have other diverse roles. Although most NRs are directly activated by ligand binding, which induces cascades of events leading to gene transcription, some NRs are also phosphorylated. Despite extensive investigations, primarily focusing on unique phosphorylation of amino acid residues in different NRs, the role of phosphorylation in the biological activity of NRs in vivo has not been firmly established. Recent studies on the phosphorylation of conserved phosphorylation motifs within the DNA- and ligand-binding domains confirmed has indicated the physiologically relevance of NR phosphorylation. This review focuses on estrogen and androgen receptors, and highlights the concept of phosphorylation as a drug target.
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Affiliation(s)
- Sawako Shindo
- Department of Environmental Toxicology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Satoru Kakizaki
- Department of Clinical Research, National Hospital Organization Takasaki General Medical Center, 36 Takamatsu-cho, Takasaki, Gunma 370-0829, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yuki Kawasaki
- Laboratory of Public Health, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaourui-machi, Takasaki, Gunma 370-0033, Japan
| | - Tsutomu Sakuma
- School of Pharmaceutical Sciences, Ohu University, Koriyama, Fukushima 963-8611, Japan
| | - Masahiko Negishi
- Reproductive and Developmental Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Ryota Shizu
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
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16
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Rola A, Palacios O, Capdevila M, Valensin D, Gumienna-Kontecka E, Potocki S. Histidine-Rich C-Terminal Tail of Mycobacterial GroEL1 and Its Copper Complex─The Impact of Point Mutations. Inorg Chem 2023; 62:6893-6908. [PMID: 37092705 PMCID: PMC10170517 DOI: 10.1021/acs.inorgchem.2c04486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The mycobacterial histidine-rich GroEL1 protein differs significantly compared to the well-known methionine/glycine-rich GroEL chaperonin. It was predicted that mycobacterial GroEL1 can play a significant role in the metal homeostasis of Mycobacteria but not, as its analogue, in protein folding. In this paper, we present the properties of the GroEL1 His-rich C-terminus as a ligand for Cu(II) ions. We studied the stoichiometry, stability, and spectroscopic features of copper complexes of the eight model peptides: L1─Ac-DHDHHHGHAH, L2─Ac-DKPAKAEDHDHHHGHAH, and six mutants of L2 in the pH range of 2-11. We revealed the impact of adjacent residues to the His-rich fragment on the complex stability: the presence of Lys and Asp residues significantly increases the stability of the system. The impact of His mutations was also examined: surprisingly, the exchange of each single His to the Gln residue did not disrupt the ability of the ligand to provide three binding sites for Cu(II) ions. Despite the most possible preference of the Cu(II) ion for the His9-His13 residues (Ac-DKPAKAEDHDHHH-) of the model peptide, especially the His11 residue, the study shows that there is not only one possible binding mode for Cu(II). The significance of this phenomenon is very important for the GroEL1 function─if the single mutation occurs naturally, the protein would be still able to interact with the metal ion.
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Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Oscar Palacios
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Merce Capdevila
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | | | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
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17
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Wiman E, Zattarin E, Aili D, Bengtsson T, Selegård R, Khalaf H. Development of novel broad-spectrum antimicrobial lipopeptides derived from plantaricin NC8 β. Sci Rep 2023; 13:4104. [PMID: 36914718 PMCID: PMC10011573 DOI: 10.1038/s41598-023-31185-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Bacterial resistance towards antibiotics is a major global health issue. Very few novel antimicrobial agents and therapies have been made available for clinical use during the past decades, despite an increasing need. Antimicrobial peptides have been intensely studied, many of which have shown great promise in vitro. We have previously demonstrated that the bacteriocin Plantaricin NC8 αβ (PLNC8 αβ) from Lactobacillus plantarum effectively inhibits Staphylococcus spp., and shows little to no cytotoxicity towards human keratinocytes. However, due to its limitations in inhibiting gram-negative species, the aim of the present study was to identify novel antimicrobial peptidomimetic compounds with an enhanced spectrum of activity, derived from the β peptide of PLNC8 αβ. We have rationally designed and synthesized a small library of lipopeptides with significantly improved antimicrobial activity towards both gram-positive and gram-negative bacteria, including the ESKAPE pathogens. The lipopeptides consist of 16 amino acids with a terminal fatty acid chain and assemble into micelles that effectively inhibit and kill bacteria by permeabilizing their cell membranes. They demonstrate low hemolytic activity and liposome model systems further confirm selectivity for bacterial lipid membranes. The combination of lipopeptides with different antibiotics enhanced the effects in a synergistic or additive manner. Our data suggest that the novel lipopeptides are promising as future antimicrobial agents, however additional experiments using relevant animal models are necessary to further validate their in vivo efficacy.
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Affiliation(s)
- Emanuel Wiman
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden
| | - Elisa Zattarin
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Daniel Aili
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Torbjörn Bengtsson
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden
| | - Robert Selegård
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden.
| | - Hazem Khalaf
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden.
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18
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Silva FA, Souza ÉMS, Ramos E, Freitas L, Nery MF. The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism. Sci Rep 2023; 13:67. [PMID: 36658131 PMCID: PMC9852289 DOI: 10.1038/s41598-022-24529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2022] [Indexed: 01/21/2023] Open
Abstract
Cetaceans are a group of aquatic mammals with the largest body sizes among living animals, including giant representatives such as blue and fin whales. To understand the genetic bases of gigantism in cetaceans, we performed molecular evolutionary analyses on five genes (GHSR, IGF2, IGFBP2, IGFBP7, and EGF) from the growth hormone/insulin-like growth factor axis, and four genes (ZFAT, EGF, LCORL, and PLAG1) previously described as related to the size of species evolutionarily close to cetaceans, such as pigs, cows, and sheep. Our dataset comprised 19 species of cetaceans, seven of which are classified as giants because they exceed 10 m in length. Our results revealed signs of positive selection in genes from the growth hormone/insulin-like growth factor axis and also in those related to body increase in cetacean-related species. In addition, pseudogenization of the EGF gene was detected in the lineage of toothless cetaceans, Mysticeti. Our results suggest the action of positive selection on gigantism in genes that act both in body augmentation and in mitigating its consequences, such as cancer suppression when involved in processes such as division, migration, and cell development control.
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Affiliation(s)
- Felipe André Silva
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Érica M. S. Souza
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Elisa Ramos
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Lucas Freitas
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Mariana F. Nery
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
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19
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Intact Transition Epitope Mapping-Force Differences between Original and Unusual Residues (ITEM-FOUR). Biomolecules 2023; 13:biom13010187. [PMID: 36671572 PMCID: PMC9856199 DOI: 10.3390/biom13010187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Antibody-based point-of-care diagnostics have become indispensable for modern medicine. In-depth analysis of antibody recognition mechanisms is the key to tailoring the accuracy and precision of test results, which themselves are crucial for targeted and personalized therapy. A rapid and robust method is desired by which binding strengths between antigens and antibodies of concern can be fine-mapped with amino acid residue resolution to examine the assumedly serious effects of single amino acid polymorphisms on insufficiencies of antibody-based detection capabilities of, e.g., life-threatening conditions such as myocardial infarction. The experimental ITEM-FOUR approach makes use of modern mass spectrometry instrumentation to investigate intact immune complexes in the gas phase. ITEM-FOUR together with molecular dynamics simulations, enables the determination of the influences of individually exchanged amino acid residues within a defined epitope on an immune complex's binding strength. Wild-type and mutated epitope peptides were ranked according to their experimentally determined dissociation enthalpies relative to each other, thereby revealing which single amino acid polymorphism caused weakened, impaired, and even abolished antibody binding. Investigating a diagnostically relevant human cardiac Troponin I epitope for which seven nonsynonymous single nucleotide polymorphisms are known to exist in the human population tackles a medically relevant but hitherto unsolved problem of current antibody-based point-of-care diagnostics.
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20
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Aróstica M, Rojas R, Aguilar LF, Carvajal-Rondanelli P, Albericio F, Guzmán F, Cárdenas C. Arginine Homopeptide of 11 Residues as a Model of Cell-Penetrating Peptides in the Interaction with Bacterial Membranes. MEMBRANES 2022; 12:1180. [PMID: 36557087 PMCID: PMC9788509 DOI: 10.3390/membranes12121180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Cell-penetrating peptides rich in arginine are good candidates to be considered as antibacterial compounds, since peptides have a lower chance of generating resistance than commonly used antibiotics. Model homopeptides are a useful tool in the study of activity and its correlation with a secondary structure, constituting an initial step in the construction of functional heteropeptides. In this report, the 11-residue arginine homopeptide (R11) was used to determine its antimicrobial activity against Staphylococcus aureus and Escherichia coli and the effect on the secondary structure, caused by the substitution of the arginine residue by the amino acids Ala, Pro, Leu and Trp, using the scanning technique. As a result, most of the substitutions improved the antibacterial activity, and nine peptides were significantly more active than R11 against the two tested bacteria. The cell-penetrating characteristic of the peptides was verified by SYTOX green assay, with no disruption to the bacterial membranes. Regarding the secondary structure in four different media-PBS, TFE, E. coli membrane extracts and DMPG vesicles-the polyproline II structure, the one of the parent R11, was not altered by unique substitutions, although the secondary structure of the peptides was best defined in E. coli membrane extract. This work aimed to shed light on the behavior of the interaction model of penetrating peptides and bacterial membranes to enhance the development of functional heteropeptides.
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Affiliation(s)
- Mónica Aróstica
- Doctorado en Biotecnología, Pontificia Universidad Católica de Valparaíso y Universidad Técnica Federico Santa María, Valparaíso 2373223, Chile
| | - Roberto Rojas
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Sede Los Castaños, 7 Norte 1348, Viña del Mar 2531098, Chile
| | - Luis Felipe Aguilar
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330, Valparaíso 2373223, Chile
| | - Patricio Carvajal-Rondanelli
- Escuela de Alimentos, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Waddington 716, Valparaíso 2360100, Chile
| | - Fernando Albericio
- Department of Organic Chemistry and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, Martí i Franqués, 1, 08028 Barcelona, Spain
- School of Chemistry, University of KwaZulu-Natal, King Edward Avenue, Scottsville, Durban 4001, South Africa
| | - Fanny Guzmán
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330, Valparaíso 2373223, Chile
| | - Constanza Cárdenas
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Av. Universidad 330, Valparaíso 2373223, Chile
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21
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Song L, Yao X, Li H, Peng B, Boka AP, Liu Y, Chen G, Liu Z, Mathias KM, Xia L, Li Q, Mir M, Li Y, Li H, Wan L. Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Mol Cell 2022; 82:4080-4098.e12. [PMID: 36272410 PMCID: PMC10071517 DOI: 10.1016/j.molcel.2022.09.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Growing evidence suggests prevalence of transcriptional condensates on chromatin, yet their mechanisms of formation and functional significance remain largely unclear. In human cancer, a series of mutations in the histone acetylation reader ENL create gain-of-function mutants with increased transcriptional activation ability. Here, we show that these mutations, clustered in ENL's structured acetyl-reading YEATS domain, trigger aberrant condensates at native genomic targets through multivalent homotypic and heterotypic interactions. Mechanistically, mutation-induced structural changes in the YEATS domain, ENL's two disordered regions of opposing charges, and the incorporation of extrinsic elongation factors are all required for ENL condensate formation. Extensive mutagenesis establishes condensate formation as a driver of oncogenic gene activation. Furthermore, expression of ENL mutants beyond the endogenous level leads to non-functional condensates. Our findings provide new mechanistic and functional insights into cancer-associated condensates and support condensate dysregulation as an oncogenic mechanism.
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Affiliation(s)
- Lele Song
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xinyi Yao
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hangpeng Li
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Peng
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiman Liu
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Guochao Chen
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zhenyang Liu
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kaeli M Mathias
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lingbo Xia
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of the School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qinglan Li
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Liling Wan
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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22
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Sato T, Shizu R, Miura Y, Hosaka T, Kanno Y, Sasaki T, Yoshinari K. Development of a strategy to identify and evaluate direct and indirect activators of constitutive androstane receptor in rats. Food Chem Toxicol 2022; 170:113510. [DOI: 10.1016/j.fct.2022.113510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
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23
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Öten AM, Atak E, Taktak Karaca B, Fırtına S, Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2124111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Ahmet Melih Öten
- Biology Education Center, Faculty of Science and Technology, Uppsala University, Uppsala, Sweden
| | - Evren Atak
- Bioinformatics and System Biology, Bioengineering Department, Gebze Technical University, Kocaeli, Turkey
| | - Banu Taktak Karaca
- Molecular Biology & Genetics Department, Faculty of Natural Science and Engineering, Atlas University, Istanbul, Turkey
| | - Sinem Fırtına
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
| | - Aslı Kutlu
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
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Muindi MP, Lee JH, Kweon H, Kasina M. Effect of Extraction Ingredients on the Conformation and Stability of Silk Sericin (SS). Polymers (Basel) 2022; 14:polym14194118. [PMID: 36236065 PMCID: PMC9572401 DOI: 10.3390/polym14194118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Silk sericin (SS) has different physicochemical properties depending on the extraction technique. In this study, SS was isolated in the presence of ingredients, including 5 to 10% ethanol (EtOH) and 5 to 10% glycine. Furthermore, temperature conditions of 80 °C, 100 °C, and 120 °C were used for 1, 3, and 5 h to evaluate the extraction rates. The extraction, gelation, structural, and cytotoxicity properties of SS extracted under different conditions were investigated. Extraction at 100 °C and 120 °C were found to have the highest SS yield, with 80 °C being the lowest. SS isolated at 100 °C and 120 °C for 1 and 3 h in water, and EtOH gelled at 4 °C in 2 to 3 days and 37 °C in 40 min. Glycine SS extracts were obtained at 100 °C and 120 °C for 1 h, gelled at 4 °C for 20 days and 37 °C for 16 h. SS was observed at 80 °C, with no gelation occurring. Glycine SS extracts obtained for 3, and 5 h at 120 °C showed no gelation. Circular dichroism (CD) results show glycine in SS induces α-helix and random coil structure. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and fast performance liquid chromatography (FPLC) were used to quantify the molecular weight distribution at 63 and 70 kDa, respectively. The MMT assay (3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) revealed no cytotoxicity in macrophage RAW 264.7 cells treated with this method SS; these findings present the significance and possibility of using selected extraction ingredients in SS that allow for the application of native SS at an initial extraction viscosity.
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Affiliation(s)
- Munguti Peter Muindi
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
| | - Ji Hae Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - HaeYong Kweon
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - Muo Kasina
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
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25
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Pierrat X, Pham A, Wong JPH, Al-Mayyah Z, Persat A. Engineering Agrobacterium tumefaciens Adhesion to Target Cells. ACS Synth Biol 2022; 11:2662-2671. [PMID: 35881049 DOI: 10.1021/acssynbio.2c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Agrobacterium tumefaciens is a plant pathogen commonly repurposed for genetic modification of crops. Despite its versatility, it remains inefficient at transferring DNA to many hosts, including to animal cells. Like many pathogens, physical contact between A. tumefaciens and host cells promotes infection efficacy. Thus, improving the strength and specificity of A. tumefaciens to target cells has the potential for enhancing DNA transfer for biotechnological and therapeutic purposes. Here, we demonstrate a methodology for engineering genetically encoded exogeneous adhesins at the surface of A. tumefaciens. We identified an autotransporter gene we named Aat that is predicted to show canonical β-barrel and passenger domains. We engineered the β-barrel scaffold and linker (Aatβ) to display synthetic adhesins susceptible to rewire A. tumefaciens to alternative host targets. As a proof of concept, we leveraged the versatility of a VHH domain to rewire A. tumefaciens adhesion to yeast and mammalian hosts displaying a GFP target receptor. Finally, to demonstrate how synthetic A. tumefaciens adhesion can improve transfer to host cells, we showed improved protein translocation into HeLa cells using a sensitive split luciferase reporter system. Engineering A. tumefaciens adhesion has therefore a strong potential in generating complex heterogeneous cellular assemblies and in improving DNA transfer efficiency against non-natural hosts.
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Affiliation(s)
- Xavier Pierrat
- School of Life Sciences, Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Alix Pham
- School of Life Sciences, Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jeremy P H Wong
- School of Life Sciences, Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Zainebe Al-Mayyah
- School of Life Sciences, Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Alexandre Persat
- School of Life Sciences, Institute of Bioengineering and Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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26
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate). Molecules 2022; 27:molecules27093022. [PMID: 35566371 PMCID: PMC9103988 DOI: 10.3390/molecules27093022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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27
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Avramov M, Schád É, Révész Á, Turiák L, Uzelac I, Tantos Á, Drahos L, Popović ŽD. Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.). Biomolecules 2022; 12:biom12040592. [PMID: 35454181 PMCID: PMC9029825 DOI: 10.3390/biom12040592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/29/2022] Open
Abstract
Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that combines wet lab methods with bioinformatics tools to identify and analyze intrinsically disordered proteins in a non-model insect species that is cold-hardy. Due to their known resilience to the effects of extreme temperatures, these proteins likely play important roles in this insect's adaptive mechanisms to sub-zero temperatures. The approach involves IDP enrichment by sample heating and double-digestion of proteins, followed by peptide and protein identification. Next, proteins are bioinformatically analyzed for disorder content, presence of long disordered regions, amino acid composition, and processes they are involved in. Finally, IDP detection is validated with an in-house 2D PAGE. In total, 608 unique proteins were identified, with 39 being mostly disordered, 100 partially disordered, 95 nearly ordered, and 374 ordered. One-third contain at least one long disordered segment. Functional information was available for only 90 proteins with intrinsic disorders out of 312 characterized proteins. Around half of the 90 proteins are cytoskeletal elements or involved in translational processes.
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Affiliation(s)
- Miloš Avramov
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (M.A.); (I.U.)
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (É.S.); (Á.T.)
| | - Ágnes Révész
- Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Á.R.); (L.T.); (L.D.)
| | - Lilla Turiák
- Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Á.R.); (L.T.); (L.D.)
| | - Iva Uzelac
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (M.A.); (I.U.)
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (É.S.); (Á.T.)
| | - László Drahos
- Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Á.R.); (L.T.); (L.D.)
| | - Željko D. Popović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (M.A.); (I.U.)
- Correspondence:
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28
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Koch NG, Baumann T, Budisa N. Efficient Unnatural Protein Production by Pyrrolysyl-tRNA Synthetase With Genetically Fused Solubility Tags. Front Bioeng Biotechnol 2022; 9:807438. [PMID: 35284428 PMCID: PMC8905625 DOI: 10.3389/fbioe.2021.807438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/17/2021] [Indexed: 11/27/2022] Open
Abstract
Introducing non-canonical amino acids (ncAAs) by engineered orthogonal pairs of aminoacyl-tRNA synthetases and tRNAs has proven to be a highly useful tool for the expansion of the genetic code. Pyrrolysyl-tRNA synthetase (PylRS) from methanogenic archaeal and bacterial species is particularly attractive due to its natural orthogonal reactivity in bacterial and eukaryotic cells. However, the scope of such a reprogrammed translation is often limited, due to low yields of chemically modified target protein. This can be the result of substrate specificity engineering, which decreases the aminoacyl-tRNA synthetase stability and reduces the abundance of active enzyme. We show that the solubility and folding of these engineered enzymes can become a bottleneck for the production of ncAA-containing proteins in vivo. Solubility tags derived from various species provide a strategy to remedy this issue. We find the N-terminal fusion of the small metal binding protein from Nitrosomonas europaea to the PylRS sequence to improve enzyme solubility and to boost orthogonal translation efficiency. Our strategy enhances the production of site-specifically labelled proteins with a variety of engineered PylRS variants by 200–540%, and further allows triple labeling. Even the wild-type enzyme gains up to 245% efficiency for established ncAA substrates.
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Affiliation(s)
- Nikolaj G Koch
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Bioanalytik, Institut für Biotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biokatalyse, Institut für Chemie, Technische Universität Berlin, Berlin, Germany.,Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
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29
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Discovery of ultrafast myosin, its amino acid sequence, and structural features. Proc Natl Acad Sci U S A 2022; 119:2120962119. [PMID: 35173046 PMCID: PMC8872768 DOI: 10.1073/pnas.2120962119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
Cytoplasmic streaming with extremely high velocity (∼70 μm s-1) occurs in cells of the characean algae (Chara). Because cytoplasmic streaming is caused by myosin XI, it has been suggested that a myosin XI with a velocity of 70 μm s-1, the fastest myosin measured so far, exists in Chara cells. However, the velocity of the previously cloned Chara corallina myosin XI (CcXI) was about 20 μm s-1, one-third of the cytoplasmic streaming velocity in Chara Recently, the genome sequence of Chara braunii has been published, revealing that this alga has four myosin XI genes. We cloned these four myosin XI (CbXI-1, 2, 3, and 4) and measured their velocities. While the velocities of CbXI-3 and CbXI-4 motor domains (MDs) were similar to that of CcXI MD, the velocities of CbXI-1 and CbXI-2 MDs were 3.2 times and 2.8 times faster than that of CcXI MD, respectively. The velocity of chimeric CbXI-1, a functional, full-length CbXI-1 construct, was 60 μm s-1 These results suggest that CbXI-1 and CbXI-2 would be the main contributors to cytoplasmic streaming in Chara cells and show that these myosins are ultrafast myosins with a velocity 10 times faster than fast skeletal muscle myosins in animals. We also report an atomic structure (2.8-Å resolution) of myosin XI using X-ray crystallography. Based on this crystal structure and the recently published cryo-electron microscopy structure of acto-myosin XI at low resolution (4.3-Å), it appears that the actin-binding region contributes to the fast movement of Chara myosin XI. Mutation experiments of actin-binding surface loops support this hypothesis.
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30
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins. Molecules 2022; 27:molecules27041260. [PMID: 35209049 PMCID: PMC8878058 DOI: 10.3390/molecules27041260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
In this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and half-times (HT) of protein digestion. After careful analysis and the application of statistical techniques and regression models, several general conclusions could be extracted from the data. The protein form to digest the fastest was ‘emulsion’. The rate of pepsinolysis in the emulsion was largely independent of the protein type, whereas the gastric digestion of the native protein in the solution was strongly dependent on the protein type. The pepsinolysis was shown to be strongly dependent on the structural components of the proteins digested—specifically, β-sheet-inhibited and amino acid, leucine, methionine, and proline-promoted digestion. Interestingly, we found that additives included in the digestion mix to alter protein hydrolysis had, in general, a negligible effect in comparison to the clear importance of the protein form or additional treatment. Overall, the findings allowed for the targeted creation of foods for fast or slow protein digestion, depending on the nutritional needs.
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31
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Dean Cho CC, Blankenship LR, Ma X, Xu S, Liu W. The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme. J Mol Biol 2022; 434:167453. [PMID: 35033561 PMCID: PMC9018550 DOI: 10.1016/j.jmb.2022.167453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/18/2021] [Accepted: 01/09/2022] [Indexed: 11/24/2022]
Abstract
The amber suppression-based noncanonical amino acid (ncAA) mutagenesis technique has been widely used in both basic and applied research. So far more than two hundred ncAAs have been genetically encoded by amber codon in both prokaryotes and eukaryotes using wild-type and engineered pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl (PylT) pairs. Methanosarcina mazei PylRS (MmPylRS) is arguably one of two most used PylRS variants. However, it contains an unstable N-terminal domain that is usually cleaved from the full-length protein during expression and therefore leads to a low enzyme activity. We discovered that the cleavage takes place after A189 and this cleavage is inhibited when MmPylRS is co-expressed with Ca. Methanomethylophilus alvus tRNAPyl (CmaPylT). In the presence of CmaPylT, MmPylRS is cleaved after an alternative site K110. MmPylRS is active toward CmaPylT. Its combined use with CmaPylT leads to enhanced incorporation of Nε-Boc-lysine (BocK) at amber codon. To prevent MmPylRS from cleavage after A189 in the presence of its cognate M. mazei tRNAPyl (MmPylT), we introduced mutations at P188. Our results indicated that the P188G mutation stabilizes MmPylRS. We showed that the P188G mutation in wild-type MmPylRS or its engineered variants allows enhanced incorporation of BocK and other noncanonical amino acids including Nε-acetyl-lysine when they are co-expressed with MmPylT.
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Affiliation(s)
- Chia-Chuan Dean Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Lauren R Blankenship
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Xinyu Ma
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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32
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McMullen P, Qiao Q, Luozhong S, Cai L, Fang L, Shao Q, Jiang S. Motif-based zwitterionic peptides impact their structure and immunogenicity. Chem Sci 2022; 13:10961-10970. [PMID: 36320710 PMCID: PMC9491220 DOI: 10.1039/d2sc03519g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 12/18/2022] Open
Abstract
The linkage of zwitterionic peptides containing alternating glutamic acid (E) and lysine (K) amino acids exhibits protective effects on protein drugs due to their high hydration capacity. Previously, short EK peptides covering the surface of a protein drug showed significant protective effects and low immunogenicity. However, for high-molecular-weight single-chain (HMWSC) zwitterionic peptides, the incorporation of structure-disrupting amino acids such as proline (P), serine (S), and glycine (G) is necessary to improve their protective ability. Herein, we first probe the immunogenicity of eight EK-containing motif-based peptides, six of which incorporate structure-disrupting amino acids P, S, and G, linked to keyhole limpet hemocyanin (KLH). These studies uncover two sequence motifs, EKS and EKG, which show uniquely higher immunogenicity, while the other motifs, especially those containing P, exhibit lower immunogenicity. Additionally, the structure and dynamics of these sequence motifs are computationally modeled by Rosetta protein predictions and molecular dynamics (MD) simulations to predict properties of higher and lower immunogenicity peptides. These simulations revealed peptides with higher immunogenicity, namely EKS and EKG, exhibit regions of charge imbalance. Then, HMWSC zwitterionic sequences were linked to a typical protein drug, interferon-alpha 2a (IFN), which showed consistent immunogenic behaviors. Finally, epitope mapping and alanine scanning experiments using the serum collected from mice injected with HMWSC sequences also implicated a link between charge imbalance and peptide immunogenicity. Structure breaking amino acids, P, S, and G, are incorporated into low immunogenic unstructured zwitterionic peptide fusion proteins. We find unique sequence motifs that exhibit charge balanced conformations and low immunogenicity.![]()
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Affiliation(s)
- Patrick McMullen
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Qiao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Sijin Luozhong
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Lirong Cai
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Liang Fang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Shaoyi Jiang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
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33
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Chaudhary AK, Gholse A, Nagarajaram HA, Dalal AB, Gupta N, Dutta AK, Danda S, Gupta R, Sankar HV, Bhavani GS, Girisha KM, Phadke SR, Ranganath P, Bashyam MD. Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India. Am J Med Genet A 2021; 188:788-805. [PMID: 34863015 DOI: 10.1002/ajmg.a.62579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is a rare genetic disorder caused by mutational inactivation of a developmental pathway responsible for generation of tissues of ectodermal origin. The X-linked form accounts for the majority of HED cases and is caused by Ectodysplasin (EDA) pathogenic variants. We performed a combined analysis of 29 X-linked hypohidrotic ectodermal dysplasia (XLHED) families (including 12 from our previous studies). In addition to the classical triad of symptoms including loss (or reduction) of ectodermal structures, such as hair, teeth, and sweat glands, we detected additional HED-related clinical features including facial dysmorphism and hyperpigmentation in several patients. Interestingly, global developmental delay was identified as an unusual clinical symptom in many patients. More importantly, we identified 22 causal pathogenic variants that included 15 missense, four small in-dels, and one nonsense, splice site, and large deletion each. Interestingly, we detected 12 unique (India-specific) pathogenic variants. Of the 29 XLHED families analyzed, 11 (38%) harbored pathogenic variant localized to the furin cleavage site. A comparison with HGMD revealed significant differences in the frequency of missense pathogenic variants; involvement of specific exons and/or protein domains and transition/transversion ratios. A significantly higher proportion of missense pathogenic variants (33%) localized to the EDA furin cleavage when compared to HGMD (7%), of which p.R155C, p.R156C, and p.R156H were detected in three families each. Therefore, the first comprehensive analysis of XLHED from India has revealed several unique features including unusual clinical symptoms and high frequency of furin cleavage site pathogenic variants.
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Affiliation(s)
- Ajay Kumar Chaudhary
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Aishwarya Gholse
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ashwin Bhikaji Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Atanu Kumar Dutta
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Rekha Gupta
- Department of Medical Genetics, Mahatma Gandhi Medical College and Hospital, Jaipur, India
| | - Hariharan V Sankar
- Department of Pediatrics, SAT Hospital, Medical College, Trivandrum, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Shubha Rao Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Vakilian M. A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis. Clin Immunol 2021; 234:108896. [PMID: 34848356 DOI: 10.1016/j.clim.2021.108896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022]
Abstract
Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.
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Affiliation(s)
- Mehrdad Vakilian
- Department of Cell Biology, Genetics and Physiology, University of Malaga (UMA), The Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain.
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35
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Marczynski M, Kimna C, Lieleg O. Purified mucins in drug delivery research. Adv Drug Deliv Rev 2021; 178:113845. [PMID: 34166760 DOI: 10.1016/j.addr.2021.113845] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
One of the main challenges in the field of drug delivery remains the development of strategies to efficiently transport pharmaceuticals across mucus barriers, which regulate the passage and retention of molecules and particles in all luminal spaces of the body. A thorough understanding of the molecular mechanisms, which govern such selective permeability, is key for achieving efficient translocation of drugs and drug carriers. For this purpose, model systems based on purified mucins can contribute valuable information. In this review, we summarize advances that were made in the field of drug delivery research with such mucin-based model systems: First, we give an overview of mucin purification procedures and discuss the suitability of model systems reconstituted from purified mucins to mimic native mucus. Then, we summarize techniques to study mucin binding. Finally, we highlight approaches that made use of mucins as building blocks for drug delivery platforms or employ mucins as active compounds.
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36
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Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. J Chem Theory Comput 2021; 17:6491-6508. [PMID: 34506133 DOI: 10.1021/acs.jctc.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarse-grained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein-membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and cross-linking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.
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Affiliation(s)
- Lily Wang
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
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37
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Muguruza-Montero A, Ramis R, Nuñez E, R Ballesteros O, G Ibarluzea M, Araujo A, M-Alicante S, Urrutia J, Leonardo A, Bergara A, Villarroel A. Do calmodulin binding IQ motifs have built-in capping domains? Protein Sci 2021; 30:2029-2041. [PMID: 34392571 PMCID: PMC8442972 DOI: 10.1002/pro.4170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 01/28/2023]
Abstract
Most calmodulin (CaM) targets are α-helices. It is not clear if CaM induces the adoption of an α-helix configuration to its targets or if those targets are selected as they spontaneously adopt an α-helical conformation. Other than an α-helix propensity, there is a great variety of CaM targets with little more in common. One exception to this rule is the IQ site that can be recognized in a number of targets, such as those ion channels belonging to the KCNQ family. Although there is negligible sequence similarity between the IQ motif and the docking site on SK2 channels, both adopt a similar three-dimensional disposition. The isolated SK2 target presents a pre-folded core region that becomes fully α-helical upon binding to CaM. The existence of this pre-folded state suggests the occurrence of capping within CaM targets. In this review, we examine the capping properties within the residues flanking this core domain, and relate known IQ motifs and capping.
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Affiliation(s)
| | - Rafael Ramis
- Donostia International Physics Center, Donostia, Spain.,Departamento de Física, Universidad del País Vasco, UPV/EHU, Leioa, Spain
| | - Eider Nuñez
- LaboKCNQ, Barrio Sarriena, Leioa, Spain.,Instituto Biofisika, CSIC-UPV/EHU, Leioa, Spain
| | - Oscar R Ballesteros
- Centro de Física de Materiales CFM, CSIC-UPV/EHU, Donostia, Spain.,Departamento de Física, Universidad del País Vasco, UPV/EHU, Leioa, Spain
| | - Markel G Ibarluzea
- Donostia International Physics Center, Donostia, Spain.,Departamento de Física, Universidad del País Vasco, UPV/EHU, Leioa, Spain
| | - Ariane Araujo
- LaboKCNQ, Barrio Sarriena, Leioa, Spain.,Instituto Biofisika, CSIC-UPV/EHU, Leioa, Spain
| | | | - Janire Urrutia
- LaboKCNQ, Barrio Sarriena, Leioa, Spain.,Department of Physiology, Faculty of Medicine and Nursery, UPV/EHU, Leioa, Spain
| | - Aritz Leonardo
- Donostia International Physics Center, Donostia, Spain.,Departamento de Física, Universidad del País Vasco, UPV/EHU, Leioa, Spain
| | - Aitor Bergara
- Donostia International Physics Center, Donostia, Spain.,Centro de Física de Materiales CFM, CSIC-UPV/EHU, Donostia, Spain.,Departamento de Física, Universidad del País Vasco, UPV/EHU, Leioa, Spain
| | - Alvaro Villarroel
- LaboKCNQ, Barrio Sarriena, Leioa, Spain.,Instituto Biofisika, CSIC-UPV/EHU, Leioa, Spain
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38
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Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg Top Life Sci 2021; 4:307-329. [PMID: 33078839 DOI: 10.1042/etls20190164] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.
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39
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Immadisetty K, Sun B, Kekenes-Huskey PM. Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins. J Phys Chem B 2021; 125:6390-6405. [PMID: 34115511 DOI: 10.1021/acs.jpcb.1c01269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Members of the parvalbumin (PV) family of calcium (Ca2+) binding proteins (CBPs) share a relatively high level of sequence similarity. However, their Ca2+ affinities and selectivities against competing ions like Mg2+ can widely vary. We conducted molecular dynamics simulations of several α-parvalbumin (αPV) constructs with micromolar to nanomolar Ca2+ affinities to identify structural and dynamic features that contribute to their binding of ions. Specifically, we examined a D94S/G98E construct with a lower Ca2+ affinity (≈-18 kcal/mol) relative to the wild type (WT) (≈-22 kcal/mol) and an S55D/E59D variant with enhanced affinity (≈-24 kcal/mol). Additionally, we also examined the binding of Mg2+ to these isoforms, which is much weaker than Ca2+. We used mean spherical approximation (MSA) theory to evaluate ion binding thermodynamics within the proteins' EF-hand domains to account for the impact of ions' finite sizes and the surrounding electrolyte composition. While the MSA scores differentiated Mg2+ from Ca2+, they did not indicate that Ca2+ binding affinities at the binding loop differed between the PV isoforms. Instead, molecular mechanics generalized Born surface area (MM/GBSA) approximation energies, which we used to quantify the thermodynamic cost of structural rearrangement of the proteins upon binding ions, indicated that S55D/E59D αPV favored Ca2+ binding by -20 kcal/mol relative to WT versus 30 kcal/mol for D94S/G98E αPV. Meanwhile, Mg2+ binding was favored for the S55D/E59D αPV and D94S/G98E αPV variants by -18.32 and -1.65 kcal/mol, respectively. These energies implicate significant contributions to ion binding beyond oxygen coordination at the binding loop, which stemmed from changes in α-helicity, β-sheet character, and hydrogen bonding. Hence, Ca2+ affinity and selectivity against Mg2+ are emergent properties stemming from both local effects within the proteins' ion binding sites as well as non-local contributions elsewhere. Our findings broaden our understanding of the molecular bases governing αPV ion binding that are likely shared by members of the broad family of CBPs.
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Affiliation(s)
| | - Bin Sun
- Stritch School of Medicine, Maywood, Illinois 60153, United States
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40
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Emenecker RJ, Holehouse AS, Strader LC. Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis. Cell Commun Signal 2021; 19:65. [PMID: 34090478 PMCID: PMC8178893 DOI: 10.1186/s12964-021-00744-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. METHODS In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), a transcription factor integral to the auxin signaling pathway in plants. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. RESULTS Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. CONCLUSIONS IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate. Video Abstract.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
| | - Lucia C. Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130 USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130 USA
- Department of Biology, Duke University, Durham, NC 27708 USA
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41
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Morita R, Shigeta Y, Harada R. Comprehensive predictions of secondary structures for comparative analysis in different species. J Struct Biol 2021; 213:107735. [PMID: 33831508 DOI: 10.1016/j.jsb.2021.107735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Protein structures are directly linked to biological functions. However, there is a gap of knowledge between the decoded genome and the structure. To bridge the gap, we focused on the secondary structure (SS). From a comprehensive analysis of predicted SS of proteins in different types of organisms, we have arrived at the following findings: The proportions of SS in genomes were different among phylogenic domains. The distributions of strand lengths indicated structural limitations in all of the species. Different from bacteria and archaea, eukaryotes have an abundance of α-helical and random coil proteins. Interestingly, there was a relationship between SS and post-translational modifications. By calculating hydrophobicity moments of helices and strands, highly amphipathic fragments of SS were found, which might be related to the biological functions. In conclusion, comprehensive predictions of SS will provide valuable perspectives to understand the entire protein structures in genomes and will help one to discover or design functional proteins.
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Affiliation(s)
- Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan.
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan.
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42
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Therapeutic Potential of Tuna Backbone Peptide and Its Analogs: An In Vitro and In Silico Study. Molecules 2021; 26:molecules26072064. [PMID: 33916797 PMCID: PMC8038390 DOI: 10.3390/molecules26072064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Tuna backbone peptide (TBP) has been reported to exert potent inhibitory activity against lipid peroxidation in vitro. Since this bears relevant physiological implications, this study was undertaken to assess the impact of peptide modifications on its bioactivity and other therapeutic potential using in vitro and in silico approach. Some TBP analogs, despite lower purity than the parent peptide, exerted promising antioxidant activities in vitro demonstrated by ABTS radical scavenging assay and cellular antioxidant activity assay. In silico digestion of the peptides resulted in the generation of antioxidant, angiotensin-converting enzyme (ACE), and dipeptidyl peptidase-IV (DPPIV) inhibitory dipeptides. Using bioinformatics platforms, we found five stable TBP analogs that hold therapeutic potential with their predicted multifunctionality, stability, non-toxicity, and low bitterness intensity. This work shows how screening and prospecting for bioactive peptides can be improved with the use of in vitro and in silico approaches.
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43
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Baranyai Z, Biri-Kovács B, Krátký M, Szeder B, Debreczeni ML, Budai J, Kovács B, Horváth L, Pári E, Németh Z, Cervenak L, Zsila F, Méhes E, Kiss É, Vinšová J, Bősze S. Cellular Internalization and Inhibition Capacity of New Anti-Glioma Peptide Conjugates: Physicochemical Characterization and Evaluation on Various Monolayer- and 3D-Spheroid-Based in Vitro Platforms. J Med Chem 2021; 64:2982-3005. [PMID: 33719423 DOI: 10.1021/acs.jmedchem.0c01399] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Most therapeutic agents used for treating brain malignancies face hindered transport through the blood-brain barrier (BBB) and poor tissue penetration. To overcome these problems, we developed peptide conjugates of conventional and experimental anticancer agents. SynB3 cell-penetrating peptide derivatives were applied that can cross the BBB. Tuftsin derivatives were used to target the neuropilin-1 transport system for selectivity and better tumor penetration. Moreover, SynB3-tuftsin tandem compounds were synthesized to combine the beneficial properties of these peptides. Most of the conjugates showed high and selective efficacy against glioblastoma cells. SynB3 and tandem derivatives demonstrated superior cellular internalization. The penetration profile of the conjugates was determined on a lipid monolayer and Transwell co-culture system with noncontact HUVEC-U87 monolayers as simple ex vivo and in vitro BBB models. Importantly, in 3D spheroids, daunomycin-peptide conjugates possessed a better tumor penetration ability than daunomycin. These conjugates are promising tools for the delivery systems with tunable features.
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Affiliation(s)
- Zsuzsa Baranyai
- Eötvös Loránd Research Network, Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Beáta Biri-Kovács
- Eötvös Loránd Research Network, Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary.,Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Bálint Szeder
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Márta L Debreczeni
- 3rd Department of Medicine Research Laboratory, Semmelweis University, Kútvölgyi út 4, H-1125 Budapest, Hungary
| | - Johanna Budai
- Eötvös Loránd Research Network, Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Bence Kovács
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4, H-2163 Vácrátót, Hungary
| | - Lilla Horváth
- Eötvös Loránd Research Network, Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Edit Pári
- Laboratory of Interfaces and Nanostructures, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Zsuzsanna Németh
- 3rd Department of Medicine Research Laboratory, Semmelweis University, Kútvölgyi út 4, H-1125 Budapest, Hungary
| | - László Cervenak
- 3rd Department of Medicine Research Laboratory, Semmelweis University, Kútvölgyi út 4, H-1125 Budapest, Hungary
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Előd Méhes
- Department of Biological Physics, Institute of Physics, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Éva Kiss
- Laboratory of Interfaces and Nanostructures, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Jarmila Vinšová
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Szilvia Bősze
- Eötvös Loránd Research Network, Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
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Identification of the Primary Factors Determining theSpecificity of Human VKORC1 Recognition by Thioredoxin-Fold Proteins. Int J Mol Sci 2021; 22:ijms22020802. [PMID: 33466919 PMCID: PMC7835823 DOI: 10.3390/ijms22020802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/28/2020] [Accepted: 01/11/2021] [Indexed: 01/25/2023] Open
Abstract
Redox (reduction-oxidation) reactions control many important biological processes in all organisms, both prokaryotes and eukaryotes. This reaction is usually accomplished by canonical disulphide-based pathways involving a donor enzyme that reduces the oxidised cysteine residues of a target protein, resulting in the cleavage of its disulphide bonds. Focusing on human vitamin K epoxide reductase (hVKORC1) as a target and on four redoxins (protein disulphide isomerase (PDI), endoplasmic reticulum oxidoreductase (ERp18), thioredoxin-related transmembrane protein 1 (Tmx1) and thioredoxin-related transmembrane protein 4 (Tmx4)) as the most probable reducers of VKORC1, a comparative in-silico analysis that concentrates on the similarity and divergence of redoxins in their sequence, secondary and tertiary structure, dynamics, intraprotein interactions and composition of the surface exposed to the target is provided. Similarly, hVKORC1 is analysed in its native state, where two pairs of cysteine residues are covalently linked, forming two disulphide bridges, as a target for Trx-fold proteins. Such analysis is used to derive the putative recognition/binding sites on each isolated protein, and PDI is suggested as the most probable hVKORC1 partner. By probing the alternative orientation of PDI with respect to hVKORC1, the functionally related noncovalent complex formed by hVKORC1 and PDI was found, which is proposed to be a first precursor to probe thiol-disulphide exchange reactions between PDI and hVKORC1.
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45
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Suppahia A, Itagi P, Burris A, Kim FMG, Vontz A, Kante A, Kim S, Im W, Deeds EJ, Roelofs J. Cooperativity in Proteasome Core Particle Maturation. iScience 2020; 23:101090. [PMID: 32380419 PMCID: PMC7210456 DOI: 10.1016/j.isci.2020.101090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Proteasomes are multi-subunit protease complexes found in all domains of life. The maturation of the core particle (CP), which harbors the active sites, involves dimerization of two half CPs (HPs) and an autocatalytic cleavage that removes β propeptides. How these steps are regulated remains poorly understood. Here, we used the Rhodococcus erythropolis CP to dissect this process in vitro. Our data show that propeptides regulate the dimerization of HPs through flexible loops we identified. Furthermore, N-terminal truncations of the propeptides accelerated HP dimerization and decelerated CP auto-activation. We identified cooperativity in autocatalysis and found that the propeptide can be partially cleaved by adjacent active sites, potentially aiding an otherwise strictly autocatalytic mechanism. We propose that cross-processing during bacterial CP maturation is the underlying mechanism leading to the observed cooperativity of activation. Our work suggests that the bacterial β propeptide plays an unexpected and complex role in regulating dimerization and autocatalytic activation.
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Affiliation(s)
- Anjana Suppahia
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Pushpa Itagi
- Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA
| | - Alicia Burris
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Faith Mi Ge Kim
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Alexander Vontz
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA
| | - Anupama Kante
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Seonghoon Kim
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18105, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18105, USA; Department of Bioengineering, Lehigh University, Bethlehem, PA 18105, USA; Department of Chemistry, Lehigh University, Bethlehem, PA 18105, USA
| | - Eric J Deeds
- Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 99024, USA; Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 99024, USA.
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA.
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Anggayasti WL, Ogino K, Yamamoto E, Helmerhorst E, Yasuoka K, Mancera RL. The acidic tail of HMGB1 regulates its secondary structure and conformational flexibility: A circular dichroism and molecular dynamics simulation study. Comput Struct Biotechnol J 2020; 18:1160-1172. [PMID: 32514327 PMCID: PMC7261955 DOI: 10.1016/j.csbj.2020.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/02/2022] Open
Abstract
High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer's disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptors (TLRs). The acidic C-terminal tail of HMGB1 is an intrinsically disordered region of the protein which is known to determine the interaction of HMGB1 to DNA and histones. This study characterizes its structural properties using a combination of circular dichroism (CD) and molecular dynamics (MD) simulations. The full-length and tail-less forms of HMGB1 were compared to rationalise the role of the acidic tail in maintaining the stability of the entire structure of HMGB1 in atomistic detail. Consistent with experimental data, the acidic tail was predicted to adopt an extended conformation that allows it to make a range of hydrogen-bonding and electrostatic interactions with the box-like domains that stabilize the overall structure of HMGB1. Absence of the acidic tail was predicted to increase structural fluctuations of all amino acids, leading to changes in secondary structure from α-helical to more hydrophilic turns along with increased exposure of multiple amino acids to the surrounding solvent. These structural changes reveal the intrinsic conformational dynamics of HMGB1 that are likely to affect the accessibility of its receptors.
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Affiliation(s)
- Wresti L. Anggayasti
- Department of Chemical Engineering, Faculty of Engineering, Brawijaya University, Jl. MT Haryono 167, Malang 65145, East Java, Indonesia
| | - Kenta Ogino
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Erik Helmerhorst
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ricardo L. Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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Drug Conjugation Induced Modulation of Structural and Membrane Interaction Features of Cationic Cell-Permeable Peptides. Int J Mol Sci 2020; 21:ijms21062197. [PMID: 32235796 PMCID: PMC7139830 DOI: 10.3390/ijms21062197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-penetrating peptides might have great potential for enhancing the therapeutic effect of drug molecules against such dangerous pathogens as Mycobacterium tuberculosis (Mtb), which causes a major health problem worldwide. A set of cationic cell-penetration peptides with various hydrophobicity were selected and synthesized as drug carrier of isoniazid (INH), a first-line antibacterial agent against tuberculosis. Molecular interactions between the peptides and their INH-conjugates with cell-membrane-forming lipid layers composed of DPPC and mycolic acid (a characteristic component of Mtb cell wall) were evaluated, using the Langmuir balance technique. Secondary structure of the INH conjugates was analyzed and compared to that of the native peptides by circular dichroism spectroscopic experiments performed in aqueous and membrane mimetic environment. A correlation was found between the conjugation induced conformational and membrane affinity changes of the INH-peptide conjugates. The degree and mode of interaction were also characterized by AFM imaging of penetrated lipid layers. In vitro biological evaluation was performed with Penetratin and Transportan conjugates. Results showed similar internalization rate into EBC-1 human squamous cell carcinoma, but markedly different subcellular localization and activity on intracellular Mtb.
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Veno J, Rahman RNZRA, Masomian M, Ali MSM, Kamarudin NHA. Insight into Improved Thermostability of Cold-Adapted Staphylococcal Lipase by Glycine to Cysteine Mutation. Molecules 2019; 24:molecules24173169. [PMID: 31480403 PMCID: PMC6749283 DOI: 10.3390/molecules24173169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022] Open
Abstract
Thermostability remains one of the most desirable traits in many lipases. Numerous studies have revealed promising strategies to improve thermostability and random mutagenesis often leads to unexpected yet interesting findings in engineering stability. Previously, the thermostability of C-terminal truncated cold-adapted lipase from Staphylococcus epidermidis AT2 (rT-M386) was markedly enhanced by directed evolution. The newly evolved mutant, G210C, demonstrated an optimal temperature shift from 25 to 45 °C and stability up to 50 °C. Interestingly, a cysteine residue was randomly introduced on the loop connecting the two lids and accounted for the only cysteine found in the lipase. We further investigated the structural and mechanistic insights that could possibly cause the significant temperature shift. Both rT-M386 and G210C were modeled and simulated at 25 °C and 50 °C. The results clearly portrayed the effect of cysteine substitution primarily on the lid stability. Comparative molecular dynamics simulation analysis revealed that G210C exhibited greater stability than the wild-type at high temperature simulation. The compactness of the G210C lipase structure increased at 50 °C and resulted in enhanced rigidity hence stability. This observation is supported by the improved and stronger non-covalent interactions formed in the protein structure. Our findings suggest that the introduction of a single cysteine residue at the lid region of cold-adapted lipase may result in unexpected increased in thermostability, thus this approach could serve as one of the thermostabilization strategies in engineering lipase stability.
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Affiliation(s)
- Jiivittha Veno
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Malihe Masomian
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Centre of Vaccine Research, School of Science and Technology, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Rossi D, Gigli L, Gamberucci A, Bordoni R, Pietrelli A, Lorenzini S, Pierantozzi E, Peretto G, De Bellis G, Della Bella P, Ferrari M, Sorrentino V, Benedetti S, Sala S, Di Resta C. A novel homozygous mutation in the TRDN gene causes a severe form of pediatric malignant ventricular arrhythmia. Heart Rhythm 2019; 17:296-304. [PMID: 31437535 DOI: 10.1016/j.hrthm.2019.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Triadin is a protein expressed in cardiac and skeletal muscle that has an essential role in the structure and functional regulation of calcium release units and excitation-contraction coupling. Mutations in the triadin gene (TRDN) have been described in different forms of human arrhythmia syndromes with early onset and severe arrhythmogenic phenotype, including triadin knockout syndrome. OBJECTIVE The purpose of this study was to characterize the pathogenetic mechanism underlying a case of severe pediatric malignant arrhythmia associated with a defect in the TRDN gene. METHODS We used a trio whole exome sequencing approach to identify the genetic defect in a 2-year-old boy who had been resuscitated from sudden cardiac arrest and had frequent episodes of ventricular fibrillation and a family history positive for sudden death. We then performed in vitro functional analysis to investigate possible pathogenic mechanisms underlying this severe phenotype. RESULTS We identified a novel homozygous missense variant (p.L56P) in the TRDN gene in the proband that was inherited from the heterozygous unaffected parents. Expression of a green fluorescent protein (GFP)-tagged mutant human cardiac triadin isoform (TRISK32-L56P-GFP) in heterologous systems revealed that the mutation alters protein dynamics. Furthermore, when co-expressed with the type 2 ryanodine receptor, caffeine-induced calcium release from TRISK32-L56P-GFP was relatively lower compared to that observed with the wild-type construct. CONCLUSION The results of this study allowed us to hypothesize a pathogenic mechanism underlying this rare arrhythmogenic recessive form, suggesting that the mutant protein potentially can trigger arrhythmias by altering calcium homeostasis.
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Affiliation(s)
- Daniela Rossi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Lorenzo Gigli
- Department of Arrhythmology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Alessandra Gamberucci
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Roberta Bordoni
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy
| | - Alessandro Pietrelli
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy
| | - Stefania Lorenzini
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Enrico Pierantozzi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Giovanni Peretto
- Department of Arrhythmology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy
| | - Paolo Della Bella
- Department of Arrhythmology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Maurizio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy; Laboratory of Clinical Molecular Biology and Cytogenetics, IRCCS San Raffaele Hospital, Milan, Italy; Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cellular Biology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Sara Benedetti
- Laboratory of Clinical Molecular Biology and Cytogenetics, IRCCS San Raffaele Hospital, Milan, Italy
| | - Simone Sala
- Department of Arrhythmology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy; Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cellular Biology, IRCCS San Raffaele Hospital, Milan, Italy.
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Porntadavity S, Jeenduang N. Structure–Function Relationships of LDL Receptor Missense Mutations Using Homology Modeling. Protein J 2019; 38:447-462. [DOI: 10.1007/s10930-019-09860-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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