201
|
Meena JK, Wang JH, Neill NJ, Keough D, Putluri N, Katsonis P, Koire AM, Lee H, Bowling EA, Tyagi S, Orellana M, Dominguez-Vidaña R, Li H, Eagle K, Danan C, Chung HC, Yang AD, Wu W, Kurley SJ, Ho BM, Zoeller JR, Olson CM, Meerbrey KL, Lichtarge O, Sreekumar A, Dacso CC, Guddat LW, Rejman D, Hocková D, Janeba Z, Simon LM, Lin CY, Pillon MC, Westbrook TF. MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer. Cancer Discov 2024; 14:1699-1716. [PMID: 39193992 PMCID: PMC11372365 DOI: 10.1158/2159-8290.cd-22-0649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/12/2023] [Accepted: 05/06/2024] [Indexed: 08/29/2024]
Abstract
Upregulation of MYC is a hallmark of cancer, wherein MYC drives oncogenic gene expression and elevates total RNA synthesis across cancer cell transcriptomes. Although this transcriptional anabolism fuels cancer growth and survival, the consequences and metabolic stresses induced by excess cellular RNA are poorly understood. Herein, we discover that RNA degradation and downstream ribonucleotide catabolism is a novel mechanism of MYC-induced cancer cell death. Combining genetics and metabolomics, we find that MYC increases RNA decay through the cytoplasmic exosome, resulting in the accumulation of cytotoxic RNA catabolites and reactive oxygen species. Notably, tumor-derived exosome mutations abrogate MYC-induced cell death, suggesting excess RNA decay may be toxic to human cancers. In agreement, purine salvage acts as a compensatory pathway that mitigates MYC-induced ribonucleotide catabolism, and inhibitors of purine salvage impair MYC+ tumor progression. Together, these data suggest that MYC-induced RNA decay is an oncogenic stress that can be exploited therapeutically. Significance: MYC is the most common oncogenic driver of poor-prognosis cancers but has been recalcitrant to therapeutic inhibition. We discovered a new vulnerability in MYC+ cancer where MYC induces cell death through excess RNA decay. Therapeutics that exacerbate downstream ribonucleotide catabolism provide a therapeutically tractable approach to TNBC (Triple-negative Breast Cancer) and other MYC-driven cancers.
Collapse
Affiliation(s)
- Jitendra K Meena
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Jarey H Wang
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Nicholas J Neill
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Dianne Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Amanda M Koire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hyemin Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Bowling
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Siddhartha Tyagi
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Mayra Orellana
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Rocio Dominguez-Vidaña
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Heyuan Li
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Kenneth Eagle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Charles Danan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hsiang-Ching Chung
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Andrew D Yang
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - William Wu
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Sarah J Kurley
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Brian M Ho
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Joseph R Zoeller
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Calla M Olson
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Kristen L Meerbrey
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Clifford C Dacso
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lukas M Simon
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
| | - Charles Y Lin
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Monica C Pillon
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Thomas F Westbrook
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
202
|
David A, Golparian D, Jacobsson S, Stratton C, Lan PT, Shimuta K, Sonnenberg P, Field N, Ohnishi M, Davies C, Unemo M. In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions. J Antimicrob Chemother 2024; 79:2221-2226. [PMID: 39004438 PMCID: PMC11368423 DOI: 10.1093/jac/dkae217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/05/2024] [Indexed: 07/16/2024] Open
Abstract
OBJECTIVES The novel dual-target triazaacenaphthylene, gepotidacin, recently showed promising results in its Phase III randomized controlled trial for the treatment of gonorrhoea. We investigated alterations in the gepotidacin GyrA and ParC targets in gonococci by in silico mining of publicly available global genomes (n = 33 213) and determined gepotidacin MICs in isolates with GyrA A92 alterations combined with other GyrA and/or ParC alterations. METHODS We examined gonococcal gyrA and parC alleles available at the European Nucleotide Archive. MICs were determined using the agar dilution method (gepotidacin) or Etest (four antimicrobials). Models of DNA gyrase and topoisomerase IV were obtained from AlphaFold and used to model gepotidacin in the binding site. RESULTS GyrA A92 alterations were identified in 0.24% of genomes: GyrA A92P/S/V + S91F + D95Y/A/N (0.208%), A92P + S91F (0.024%) and A92P (0.003%), but no A92T (previously associated with gepotidacin resistance) was found. ParC D86 alterations were found in 10.6% of genomes: ParC D86N/G (10.5%), D86N + S87I (0.051%), D86N + S88P (0.012%) and D86G + E91G (0.003%). One isolate had GyrA A92P + ParC D86N alterations, but remained susceptible to gepotidacin (MIC = 0.125 mg/L). No GyrA plus ParC alterations resulted in a gepotidacin MIC > 4 mg/L. Modelling of gepotidacin binding to GyrA A92/A92T/A92P suggested that gepotidacin resistance due to GyrA A92T might be linked to the formation of a new polar contact with DNA. CONCLUSIONS In silico mining of 33 213 global gonococcal genomes (isolates from 1928 to 2023) showed that A92 is highly conserved in GyrA, while alterations in D86 of ParC are common. No GyrA plus ParC alterations caused gepotidacin resistance. MIC determination and genomic surveillance of potential antimicrobial resistance determinants are imperative.
Collapse
Affiliation(s)
- Alexandra David
- Institute for Global Health, Faculty of Population Health, University College London, London, UK
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Caleb Stratton
- Department of Biochemistry and Molecular Biology, University of South Alabama, AL, USA
| | - Pham Thi Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Pam Sonnenberg
- Institute for Global Health, Faculty of Population Health, University College London, London, UK
| | - Nigel Field
- Institute for Global Health, Faculty of Population Health, University College London, London, UK
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, University of South Alabama, AL, USA
| | - Magnus Unemo
- Institute for Global Health, Faculty of Population Health, University College London, London, UK
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
203
|
Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024; 123:2790-2806. [PMID: 38297834 PMCID: PMC11393682 DOI: 10.1016/j.bpj.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
Collapse
Affiliation(s)
- Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Gemechis D Degaga
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Wei Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
| |
Collapse
|
204
|
Chen J, Xu Y, Yang X, Cang Z, Geng W, Wei GW. Poisson-Boltzmann-based machine learning model for electrostatic analysis. Biophys J 2024; 123:2807-2814. [PMID: 38356263 PMCID: PMC11393697 DOI: 10.1016/j.bpj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic solvation free energies for macromolecules due to the nonlinearity, dielectric jumps, charge singularity, and geometric complexity associated with the PB equation. The present work introduces a PB-based machine learning (PBML) model for biomolecular electrostatic analysis. Trained with the second-order accurate MIBPB solver, the proposed PBML model is found to be more accurate and faster than several eminent PB solvers in electrostatic analysis. The proposed PBML model can provide highly accurate PB electrostatic solvation free energy of new biomolecules or new conformations generated by molecular dynamics with much reduced computational cost.
Collapse
Affiliation(s)
- Jiahui Chen
- Department of Mathematics, University of Arkansas, Fayetteville, Arkansas
| | | | - Xin Yang
- Department of Mathematics, Southern Methodist University, Dallas, Texas
| | - Zixuan Cang
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina
| | - Weihua Geng
- Department of Mathematics, Southern Methodist University, Dallas, Texas.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, Michigan; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.
| |
Collapse
|
205
|
Zhao X, Du J, Sun W, Fan J, Peng X. Regulating Charge Transfer in Cyanine Dyes: A Universal Methodology for Enhancing Cancer Phototherapeutic Efficacy. Acc Chem Res 2024; 57:2582-2593. [PMID: 39152945 DOI: 10.1021/acs.accounts.4c00399] [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: 08/19/2024]
Abstract
ConspectusDue to the advantages of spatiotemporal selectivity and inherent noninvasiveness, cancer phototherapy, which includes both photodynamic therapy (PDT) and photothermal therapy (PTT), has garnered significant attention in recent years as a promising cancer treatment. Despite the commendable progress in this field, persistent challenges remain. In PDT, limitations in dyes manifest as low intersystem crossing (ISC) efficiency and oxygen-dependent photoactivity, resulting in unsatisfactory performance, particularly under hypoxic conditions. Similarly, PTT encounters consistent insufficiencies in the photothermal conversion efficiency (PCE) of dyes. Additionally, the suboptimal phototherapeutic efficacy often exhibits a limited immune response. These factors collectively impose significant constraints on phototherapy in oncological applications, leading to limited tumor inhibition, tumor recurrence, and even metastasis.Unlike strategies that rely on external assistance with complicated systems, manipulating excited-state deactivation pathways in biocompatible dyes offers a universal way to systematically address these challenges. Our group has devoted considerable effort to achieving this goal. In this Account, we present and discuss our journey in optimizing excited-state energy-release pathways through regulating molecular charge transfer based on cyanine dyes, which are renowned for their exceptional photophysical properties and harmonious biocompatibility. The investigation begins with the introduction of amino groups in the meso position of a heptamethine cyanine dye, where the intramolecular charge transfer (ICT) effect causes a significant enlargement of the Stokes shift. Subsequently, ICT induced by introducing functional electron-deficient groups in cyanines is found to decrease the overlap of electron distribution or narrow the energy gaps of molecular frontier orbitals. Such modifications result in a reduction of the energy gaps between singlet and triplet states or an improvement in internal conversion, ultimately promoting phototherapy efficacy in both primary and distant tumors. Furthermore, with the intensification of the charge transfer effect aided by light, photoinduced intramolecular electron transfer occurs in some cyanines, leading to complete charge separation in the excited state. This process enhances the transition to the ground or triplet states, improving tumor phototherapy and inhibiting metastasis by increasing the PCE or the yield of reactive oxygen species, respectively. Shifting focus from intramolecular to intermolecular interactions, we successfully constructed and explored cyanines based on intermolecular charge transfer. These dyes, with excited-state dynamics mimicking natural photosynthesis, generate radicals and facilitate oxygen-independent hypoxic tumor PDT. Finally, we outlined the existing challenges and future directions for optimizing phototherapeutic efficacy by regulating molecular charge transfer. This Account provides molecular-level insights into improving phototherapeutic performance, offering valuable perspectives, and inspiring the development of functional dyes in other application fields.
Collapse
Affiliation(s)
- Xueze Zhao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
- Ningbo Institute of Dalian University of Technology, No. 26 Yucai Road, 315016 Ningbo, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
| |
Collapse
|
206
|
Guo W, Du D, Zhang H, Sanchez JE, Sun S, Xu W, Peng Y, Li L. Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule. Biophys J 2024; 123:2740-2748. [PMID: 38160255 PMCID: PMC11393710 DOI: 10.1016/j.bpj.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/26/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions that are bound or restricted at the Ncd-tubulin dimer binding interfaces. To consider the ion effects, widely used implicit solvent models treat ions implicitly in the continuous solvent environment without focusing on the individual ions' effects. But highly charged biomolecules such as the Ncd and tubulin dimer may capture some ions at highly charged regions as bound ions. Such bound ions are restricted to their binding sites; thus, they can be treated as part of the biomolecules. By applying multiscale computational methods, including the machine-learning-based Hybridizing Ions Treatment-2 program, molecular dynamics simulations, DelPhi, and DelPhiForce, we studied the interaction between the Ncd motor domain and the tubulin dimer using a hybrid solvent model, which considers the bound ions explicitly and the other ions implicitly in the solvent environment. To identify the importance of treating bound ions explicitly, we also performed calculations using the implicit solvent model without considering the individual bound ions. We found that the calculations of the electrostatic features differ significantly between those of the hybrid solvent model and the pure implicit solvent model. The analyses show that treating bound ions at highly charged regions explicitly is crucial for electrostatic calculations. This work proposes a machine-learning-based approach to handle the bound ions using the hybrid solvent model. Such an approach is not only capable of handling kinesin-tubulin complexes but is also appropriate for other highly charged biomolecules, such as DNA/RNA, viral capsid proteins, etc.
Collapse
Affiliation(s)
- Wenhan Guo
- College of Physical Science and Technology, Central China Normal University, Hubei, China; Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Dan Du
- Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Houfang Zhang
- College of Physical Science and Technology, Central China Normal University, Hubei, China
| | - Jason E Sanchez
- Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Shengjie Sun
- Computational Science Program, University of Texas at El Paso, El Paso, Texas; School of Life Sciences, Central South University, Hunan, China
| | - Wang Xu
- College of Physical Science and Technology, Central China Normal University, Hubei, China
| | - Yunhui Peng
- College of Physical Science and Technology, Central China Normal University, Hubei, China.
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, Texas; Department of Physics, University of Texas at El Paso, El Paso, Texas.
| |
Collapse
|
207
|
Nowak R, Gazecka M, Hoffmann M, Kierzek R, Pöhlmann S, Zmora P. TMPRSS2-specific antisense oligonucleotides inhibit host cell entry of emerging viruses. Virology 2024; 600:110218. [PMID: 39276670 DOI: 10.1016/j.virol.2024.110218] [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: 03/14/2024] [Revised: 08/06/2024] [Accepted: 08/30/2024] [Indexed: 09/17/2024]
Abstract
Emerging viruses, such as novel influenza A viruses (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), pose a constant threat to animal and human health. Identification of host cell factors necessary for viral replication but dispensable for cellular survival might reveal novel, attractive targets for therapeutic intervention. Proteolytic activation of IAV hemagglutinin (HA) and SARS-CoV-2 spike protein (S) by the type II transmembrane serine protease (TTSPs), e.g. TMPRSS2 is sought to be critical for viral spread and pathogenesis. Here, we investigated the secondary structure of TMPRSS2 mRNA coding sequence and designed TMPRSS2-specific antisense oligonucleotides (ASOs). Several of these ASOs markedly reduced the TMPRSS2 expression and decreased IAV infection and SARS-CoV-2 entry into cells.
Collapse
Affiliation(s)
- Rafal Nowak
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Monika Gazecka
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg August University, Göttingen, Germany
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg August University, Göttingen, Germany
| | - Pawel Zmora
- Department of Molecular Virology, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland.
| |
Collapse
|
208
|
Sahu R, Yamijala SSRKC, Rao KV, Reddy SK. Dispersion-Driven Cooperativity in Alkyl Perylene Diimide Oligomers: Insights from Density Functional Theory. Chemphyschem 2024; 25:e202400235. [PMID: 38807431 DOI: 10.1002/cphc.202400235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024]
Abstract
The cooperative mechanism is of paramount importance in the synthesis of supramolecular polymers with desired characteristics, including molecular mass, polydispersity, and morphology. It is primarily driven by the presence of intermolecular interactions, which encompass strong hydrogen bonding, metal-ligand interactions, and dipole-dipole interactions. In this study, we utilize density functional theory and energy decomposition analysis to investigate the cooperative behavior of perylene diimide (PDI) oligomers with alkyl chains at their imide positions, which lack the previously mentioned interactions. Our systematic examination reveals that dispersion interactions originating from the alkyl side-chain substituents play an important role in promoting cooperativity within these PDIs. This influence becomes even more pronounced for alkyl chain lengths beyond hexyl groups. The energy decomposition analysis reveals that the delicate balance between dispersion energy and Pauli repulsion energy is the key driver of cooperative behavior in PDIs. Additionally, we have developed a mathematical model capable of predicting the saturated binding energies for PDI oligomers of varying sizes and alkyl chain lengths. Overall, our findings emphasize the previously undervalued significance of dispersion forces in cooperative supramolecular polymerization, enhancing our overall understanding of the cooperative mechanism.
Collapse
Affiliation(s)
- Rahul Sahu
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, Pin, 721302, India
| | - Sharma S R K C Yamijala
- Department of Chemistry, Centre for Atomistic Modelling and Materials Design, Centre for Quantum Information, Communication, and Computing, Centre for Molecular Materials and Functions, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, Pin, India
- Centre for Atomistic Modelling and Materials Design, Indian Institute of Technology Madras, Chennai, Tamil Nadu, Pin, 600036, India
- Centre for Quantum Information, Communication, and Computing, Indian Institute of Technology Madras, Chennai, Tamil Nadu, Pin, 600036, India
- Centre for Molecular Materials and Functions, Indian Institute of Technology Madras, Chennai, Tamil Nadu, Pin, 600036, India
| | - Kotagiri Venkata Rao
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, Pin, 502285, India
| | - Sandeep K Reddy
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, Pin, 721302, India
| |
Collapse
|
209
|
Tilehkan A, Arvand M. Study on the electrochemical and spectroscopic characteristics of holmium ion and its interaction with DNA. Sci Rep 2024; 14:20383. [PMID: 39223199 PMCID: PMC11369137 DOI: 10.1038/s41598-024-71412-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Metal ion-DNA interactions play a crucial role in modulating the structure and function of genetic material in the natural environment. In this study, we report on the favorable electrochemical activity of holmium(III) (Ho3+) on a glassy carbon electrode (GCE) and its interaction with double-stranded DNA. The interaction between DNA and Ho3+ was investigated for the first time using cyclic voltammetry and differential pulse voltammetry. The electrochemical behavior of Ho3+ ions on a GCE exhibited a reversible electron transfer process, indicative of its redox activity. A linear correlation between the peak current and the square root of the scan rate was observed, suggesting a diffusion-controlled kinetic regime for the electrochemical process. Additionally, fluorescence and absorption spectroscopy were employed to confirm the binding of Ho3+ to DNA. Our findings demonstrate that, at pH 7.2, specific DNA bases and phosphate groups can interact with Ho3+ ions. Moreover, electrochemical measurements suggest that Ho3+ ions bind to DNA via a groove binding mode, with a calculated binding ratio of 1:1 between Ho3+ and DNA. Notably, under optimal conditions, an increase in the amount of DNA leads to a significant reduction in the current intensity of Ho3+ ions.
Collapse
Affiliation(s)
- Ali Tilehkan
- Electroanalytical Chemistry Laboratory, Faculty of Chemistry, University of Guilan, Namjoo Street, P.O. Box: 1914-41335, Rasht, Iran
| | - Majid Arvand
- Electroanalytical Chemistry Laboratory, Faculty of Chemistry, University of Guilan, Namjoo Street, P.O. Box: 1914-41335, Rasht, Iran.
| |
Collapse
|
210
|
Hollmann F, Sanchis J, Reetz MT. Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants. Angew Chem Int Ed Engl 2024; 63:e202404880. [PMID: 38884594 DOI: 10.1002/anie.202404880] [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: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.
Collapse
Affiliation(s)
- Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Manfred T Reetz
- Max-Plank-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45481, Mülheim, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| |
Collapse
|
211
|
Fu Y, Lin Q, Lan R, Shao Z. Ultra-Strong Protein-Based Hydrogels via Promoting Intermolecular Entanglement of the Amorphous Region. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2403376. [PMID: 39221643 DOI: 10.1002/smll.202403376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/19/2024] [Indexed: 09/04/2024]
Abstract
Proteins are classified as biopolymers which share similar structural features with semi-crystalline polymers. Although their unique biocompatibility facilitates the universal applications of protein-based hydrogels in the biomedical field, the mechanical performances of protein-based hydrogels fall short of practical requirements. Conventional strategies for enhancing mechanical properties focus on forming regularly folded secondary structures as analogs of crystalline regions. This concept is based on proteins as the analogy of semi-crystalline polymers, in which crystalline regions profoundly contribute to the mechanical performances. Even though the contribution of the amorphous region is equally weighted for semi-crystalline polymers, their capacity to improve the mechanical performances of protein-based structures is still undervalued. Herein, the potential of promoting the mechanical performances is explored by controlling the state of amorphous regions in protein-based hydrogels. A fibril protein is chosen, regenerated silk fibroin (RSF), as a model molecule for its similar viscoelasticity with a semi-crystalline polymer. The amorphous regions in the RSF hydrogels are transformed from extended to entangled states through a double-crosslinking method. The formation of entanglement integrates new physically crosslinked points for remarkable improvement in mechanical performances. A robust hydrogel is not only developed but also intended to provide new insights into the structural-property relationship of protein-based hydrogels.
Collapse
Affiliation(s)
- Yu Fu
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Qinrui Lin
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Ruoqi Lan
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, P. R. China
- Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, P. R. China
| |
Collapse
|
212
|
Rosandić M, Paar V. Maximal Genetic Code Symmetry Is a Physicochemical Purine-Pyrimidine Symmetry Language for Transcription and Translation in the Flow of Genetic Information from DNA to Proteins. Int J Mol Sci 2024; 25:9543. [PMID: 39273490 PMCID: PMC11395414 DOI: 10.3390/ijms25179543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/15/2024] Open
Abstract
Until now, research has not taken into consideration the physicochemical purine-pyrimidine symmetries of the genetic code in the transcription and translation processes of proteinogenesis. Our Supersymmetry Genetic Code table, developed in 2022, is common and unique for all RNA and DNA living species. Its basic structure is a purine-pyrimidine symmetry net with double mirror symmetry. Accordingly, the symmetry of the genetic code directly shows its organisation based on the principle of nucleotide Watson-Crick and codon-anticodon pairing. The maximal purine-pyrimidine symmetries of codons show that each codon has a strictly defined and unchangeable position within the genetic code. We discovered that the physicochemical symmetries of the genetic code play a fundamental role in recognising and differentiating codons from mRNA and the anticodon tRNA and aminoacyl-tRNA synthetases in the transcription and translation processes. These symmetries also support the wobble hypothesis with non-Watson-Crick pairing interactions between the translation process from mRNA to tRNA. The Supersymmetry Genetic Code table shows a specific arrangement of the second base of codons, according to which it is possible that an anticodon from tRNA recognises whether a codon from mRNA belongs to an amino acid with two or four codons, which is very important in the purposeful use of the wobble pairing process. Therefore, we show that canonical and wobble pairings essentially do not lead to misreading and errors during translation, and we point out the role of physicochemical purine-pyrimidine symmetries in decreasing disorder according to error minimisation and preserving the integrity of biological processes during proteinogenesis.
Collapse
Affiliation(s)
- Marija Rosandić
- Department of Internal Medicine, University Hospital Centre Zagreb, (Ret.), 10000 Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Vladimir Paar
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
- Physics Department, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| |
Collapse
|
213
|
Chiu PL, Orjuela JD, de Groot BL, Aponte Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 2024; 12:RP90851. [PMID: 39222068 PMCID: PMC11368405 DOI: 10.7554/elife.90851] [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: 09/04/2024] Open
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
Collapse
Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Juan D Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Biomedical Engineering Department, Universidad de los AndesBogotáColombia
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Camilo Aponte Santamaría
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
214
|
Izzi G, Paladino A, Oliva R, Barra G, Ruggiero A, Del Vecchio P, Vitagliano L, Graziano G. Destabilization of the D2 domain of Thermotoga maritima arginine binding protein induced by guanidinium thiocyanate and its counteraction by stabilizing agents. Protein Sci 2024; 33:e5146. [PMID: 39150147 PMCID: PMC11328109 DOI: 10.1002/pro.5146] [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: 05/17/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024]
Abstract
D2 is a structural and cooperative domain of Thermotoga maritima Arginine Binding Protein, that possesses a remarkable conformational stability, with a denaturation temperature of 102.6°C, at pH 7.4. The addition of potassium thiocyanate causes a significant decrease in the D2 denaturation temperature. The interactions of thiocyanate ions with D2 have been studied by means of isothermal titration calorimetry measurements and molecular dynamics simulations. It emerged that: (a) 20-30 thiocyanate ions interact with the D2 surface and are present in its first solvation shell; (b) each of them makes several contacts with protein groups, both polar and nonpolar ones. The addition of guanidinium thiocyanate causes a marked destabilization of the D2 native state, because both the ions are denaturing agents. However, on adding to the solution containing D2 and guanidinium thiocyanate a stabilizing agent, such as TMAO, sucrose or sodium sulfate, a significant increase in denaturation temperature occurs. The present results confirm that counteraction is a general phenomenon for globular proteins.
Collapse
Affiliation(s)
- Guido Izzi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Giovanni Barra
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento, Italy
| |
Collapse
|
215
|
Rahaman MM, Zhang S. RNAMotifProfile: a graph-based approach to build RNA structural motif profiles. NAR Genom Bioinform 2024; 6:lqae128. [PMID: 39328267 PMCID: PMC11426329 DOI: 10.1093/nargab/lqae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/24/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024] Open
Abstract
RNA structural motifs are the recurrent segments in RNA three-dimensional structures that play a crucial role in the functional diversity of RNAs. Understanding the similarities and variations within these recurrent motif groups is essential for gaining insights into RNA structure and function. While recurrent structural motifs are generally assumed to be composed of the same isosteric base interactions, this consistent pattern is not observed across all examples of these motifs. Existing methods for analyzing and comparing RNA structural motifs may overlook variations in base interactions and associated nucleotides. RNAMotifProfile is a novel profile-to-profile alignment algorithm that generates a comprehensive profile from a group of structural motifs, incorporating all base interactions and associated nucleotides at each position. By structurally aligning input motif instances using a guide-tree-based approach, RNAMotifProfile captures the similarities and variations within recurrent motif groups. Additionally, RNAMotifProfile can function as a motif search tool, enabling the identification of instances of a specific motif family by searching with the corresponding profile. The ability to generate accurate and comprehensive profiles for RNA structural motif families, and to search for these motifs, facilitates a deeper understanding of RNA structure-function relationships and potential applications in RNA engineering and therapeutic design.
Collapse
Affiliation(s)
- Md Mahfuzur Rahaman
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL 32816-2362, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL 32816-2362, USA
| |
Collapse
|
216
|
Zhu H, Liang X, Ding J, Wang J, Li P, Zhou W, Wang J, Wu FA, Sheng S. Transcriptome analysis and functional study of phospholipase A 2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae. INSECT SCIENCE 2024. [PMID: 39219288 DOI: 10.1111/1744-7917.13440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/07/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
There is abundant evidence that parasitoids manipulate their hosts by envenomation to support the development and survival of their progeny before oviposition. However, the specific mechanism underlying host nutritional manipulation remains largely unclear. To gain a more comprehensive insight into the effects induced by the gregarious ectoparasitoid Iseropus kuwanae (Hymenoptera: Ichneumonidae) on the greater wax moth Galleria mellonella (Lepidoptera: Pyralidae) larvae, we sequenced the transcriptome of both non-envenomed and envenomed G. mellonella larvae, specifically targeting genes related to lipid metabolism. The present study revealed that 202 differentially expressed genes (DEGs) were identified and 9 DEGs were involved in lipid metabolism. The expression levels of these 9 DEGs relied on envenomation and the duration post-envenomation. Further, envenomation by I. kuwanae induced an increase in triglyceride (TG) level in the hemolymph of G. mellonella larvae. Furthermore, silencing GmPLA2 in G. mellonella larvae 24 h post-envenomation significantly decreased the content of 4 unsaturated fatty acids and TG levels in the hemolymph. The content of linoleic acid and α-linoleic acid were significantly decreased and the content of oleic acid was significantly increased by exogenous supplement of arachidonic acid. Meanwhile, the reduction in host lipid levels impairs the growth and development of wasp offspring. The present study provides valuable knowledge about the molecular mechanism of the nutritional interaction between parasitoids and their hosts and sheds light on the coevolution between parasitoids and host insects.
Collapse
Affiliation(s)
- Hanqi Zhu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xinhao Liang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Jianhao Ding
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Jinzheng Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Ping Li
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Weihong Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Fu-An Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Sheng Sheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| |
Collapse
|
217
|
Rodríguez-Candela Mateos M, Carpintero-Fernández P, Freijanes PS, Mosquera J, Nebril BA, Mayán MD. Insights into the role of connexins and specialized intercellular communication pathways in breast cancer: Mechanisms and applications. Biochim Biophys Acta Rev Cancer 2024; 1879:189173. [PMID: 39154967 DOI: 10.1016/j.bbcan.2024.189173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
Gap junctions, membrane-based channels comprised of connexin proteins (Cxs), facilitate direct communication among neighbouring cells and between cells and the extracellular space through their hemichannels. The normal human breast expresses various Cxs family proteins, such as Cx43, Cx30, Cx32, Cx46, and Cx26, crucial for proper tissue development and function. These proteins play a significant role in breast cancer development, progression, and therapy response. In primary tumours, there is often a reduction and cytoplasmic mislocalization of Cx43 and Cx26, while metastatic lesions show an upregulation of these and other Cxs. Although existing research predominantly supports the tumour-suppressing role of Cxs in primary carcinomas through channel-dependent and independent functions, controversies persist regarding their involvement in the metastatic process. This review aims to provide an updated perspective on Cxs in human breast cancer, with a specific focus on intrinsic subtypes due to the heterogeneous nature of this disease. Additionally, the manuscript will explore the role of Cxs in immune interactions and novel forms of intercellular communication, such as tunneling nanotubes and extracellular vesicles, within the breast tumour context and tumour microenvironment. Recent findings suggest that Cxs hold potential as therapeutic targets for mitigating metastasis and drug resistance. Furthermore, they may serve as novel biomarkers for cancer prognosis, offering promising avenues for future research and clinical applications.
Collapse
Affiliation(s)
- Marina Rodríguez-Candela Mateos
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain
| | - Paula Carpintero-Fernández
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain; CellCOM Research Group, Center for Research in Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Edificio Olimpia Valencia, Campus Universitario Lagoas Marcosende, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS, Spain
| | - Paz Santiago Freijanes
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain; Anatomic Pathology Department, Breast Unit, A Coruña University Hospital, SERGAS, A Coruña, Spain
| | - Joaquin Mosquera
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain; Surgery Department, Breast Unit, A Coruña University Hospital, SERGAS, A Coruña, Spain
| | - Benigno Acea Nebril
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain; Surgery Department, Breast Unit, A Coruña University Hospital, SERGAS, A Coruña, Spain
| | - María D Mayán
- Instituto de Investigación Biomédica de A Coruña (INIBIC), Servizo Galego de Saúde (SERGAS), Xubias de Arriba, 84, 15006 A Coruña, Spain; CellCOM Research Group, Center for Research in Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Edificio Olimpia Valencia, Campus Universitario Lagoas Marcosende, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS, Spain.
| |
Collapse
|
218
|
Tian L, Andrews C, Yan Q, Yang JJ. Molecular regulation of calcium-sensing receptor (CaSR)-mediated signaling. Chronic Dis Transl Med 2024; 10:167-194. [PMID: 39027195 PMCID: PMC11252437 DOI: 10.1002/cdt3.123] [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: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 07/20/2024] Open
Abstract
Calcium-sensing receptor (CaSR), a family C G-protein-coupled receptor, plays a crucial role in regulating calcium homeostasis by sensing small concentration changes of extracellular Ca2+, Mg2+, amino acids (e.g., L-Trp and L-Phe), small peptides, anions (e.g., HCO3 - and PO4 3-), and pH. CaSR-mediated intracellular Ca2+ signaling regulates a diverse set of cellular processes including gene transcription, cell proliferation, differentiation, apoptosis, muscle contraction, and neuronal transmission. Dysfunction of CaSR with mutations results in diseases such as autosomal dominant hypocalcemia, familial hypocalciuric hypercalcemia, and neonatal severe hyperparathyroidism. CaSR also influences calciotropic disorders, such as osteoporosis, and noncalciotropic disorders, such as cancer, Alzheimer's disease, and pulmonary arterial hypertension. This study first reviews recent advances in biochemical and structural determination of the framework of CaSR and its interaction sites with natural ligands, as well as exogenous positive allosteric modulators and negative allosteric modulators. The establishment of the first CaSR protein-protein interactome network revealed 94 novel players involved in protein processing in endoplasmic reticulum, trafficking, cell surface expression, endocytosis, degradation, and signaling pathways. The roles of these proteins in Ca2+-dependent cellular physiological processes and in CaSR-dependent cellular signaling provide new insights into the molecular basis of diseases caused by CaSR mutations and dysregulated CaSR activity caused by its protein interactors and facilitate the design of therapeutic agents that target CaSR and other family C G-protein-coupled receptors.
Collapse
Affiliation(s)
- Li Tian
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Corey Andrews
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Qiuyun Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Advanced Translational Imaging FacilityGeorgia State UniversityAtlantaGeorgiaUSA
| |
Collapse
|
219
|
Gong X, Zhang J, Gan Q, Teng Y, Hou J, Lyu Y, Liu Z, Wu Z, Dai R, Zou Y, Wang X, Zhu D, Zhu H, Liu T, Yan Y. Advancing microbial production through artificial intelligence-aided biology. Biotechnol Adv 2024; 74:108399. [PMID: 38925317 DOI: 10.1016/j.biotechadv.2024.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/20/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for value-added compound production. To optimize metabolism and reach optimal productivity, synthetic biology has developed various genetic devices to engineer microbial systems by gene editing, high-throughput protein engineering, and dynamic regulation. However, current synthetic biology methodologies still rely heavily on manual design, laborious testing, and exhaustive analysis. The emerging interdisciplinary field of artificial intelligence (AI) and biology has become pivotal in addressing the remaining challenges. AI-aided microbial production harnesses the power of processing, learning, and predicting vast amounts of biological data within seconds, providing outputs with high probability. With well-trained AI models, the conventional Design-Build-Test (DBT) cycle has been transformed into a multidimensional Design-Build-Test-Learn-Predict (DBTLP) workflow, leading to significantly improved operational efficiency and reduced labor consumption. Here, we comprehensively review the main components and recent advances in AI-aided microbial production, focusing on genome annotation, AI-aided protein engineering, artificial functional protein design, and AI-enabled pathway prediction. Finally, we discuss the challenges of integrating novel AI techniques into biology and propose the potential of large language models (LLMs) in advancing microbial production.
Collapse
Affiliation(s)
- Xinyu Gong
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jianli Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qi Gan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yuxi Teng
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jixin Hou
- School of ECAM, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Yanjun Lyu
- Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington 76019, USA
| | - Zhengliang Liu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Zihao Wu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Runpeng Dai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yusong Zou
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Xianqiao Wang
- School of ECAM, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Dajiang Zhu
- Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington 76019, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianming Liu
- School of Computing, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
220
|
Miura K, Nakamura H. Development of carbonic anhydrase IX-targeting molecular-targeted photodynamic therapy. Bioorg Med Chem Lett 2024; 109:129821. [PMID: 38810709 DOI: 10.1016/j.bmcl.2024.129821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
The efficacy of molecular-targeted photodynamic therapy (MT-PDT) targeting carbonic anhydrase (CA) IX, a cancer-specific molecule, was demonstrated. CA ligand-directed photosensitizers 1-3 were evaluated for their ability to deactivate CAIX protein in cells. Compounds 2 and 3 selectively deactivated CAIX protein under 540 nm light without affecting internal standard proteins. Mechanistic studies revealed that compound 3 not only induced CAIX-selective light inactivation via singlet oxygen but also induced cell membrane damage, resulting in an anti-tumor effect. In vivo studies of CAIX-targeting MT-PDT revealed that treatment with compound 3 followed by light irradiation exhibited remarkable anti-tumor activity, leading to tumor degeneration and necrosis.
Collapse
Affiliation(s)
- Kazuki Miura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
| |
Collapse
|
221
|
Fuentes P, Pelletier J, Gentilella A. Decoding ribosome complexity: role of ribosomal proteins in cancer and disease. NAR Cancer 2024; 6:zcae032. [PMID: 39045153 PMCID: PMC11263879 DOI: 10.1093/narcan/zcae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/31/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024] Open
Abstract
The ribosome is a remarkably complex machinery, at the interface with diverse cellular functions and processes. Evolutionarily conserved, yet intricately regulated, ribosomes play pivotal roles in decoding genetic information into the synthesis of proteins and in the generation of biomass critical for cellular physiological functions. Recent insights have revealed the existence of ribosome heterogeneity at multiple levels. Such heterogeneity extends to cancer, where aberrant ribosome biogenesis and function contribute to oncogenesis. This led to the emergence of the concept of 'onco-ribosomes', specific ribosomal variants with altered structural dynamics, contributing to cancer initiation and progression. Ribosomal proteins (RPs) are involved in many of these alterations, acting as critical factors for the translational reprogramming of cancer cells. In this review article, we highlight the roles of RPs in ribosome biogenesis, how mutations in RPs and their paralogues reshape the translational landscape, driving clonal evolution and therapeutic resistance. Furthermore, we present recent evidence providing new insights into post-translational modifications of RPs, such as ubiquitylation, UFMylation and phosphorylation, and how they regulate ribosome recycling, translational fidelity and cellular stress responses. Understanding the intricate interplay between ribosome complexity, heterogeneity and RP-mediated regulatory mechanisms in pathology offers profound insights into cancer biology and unveils novel therapeutic avenues targeting the translational machinery in cancer.
Collapse
Affiliation(s)
- Pedro Fuentes
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
| | - Joffrey Pelletier
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08908, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Gentilella
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, 08028, Barcelona, Spain
| |
Collapse
|
222
|
Liu F, Li R, Zhu Z, Yang Y, Lu F. Current developments of gene therapy in human diseases. MedComm (Beijing) 2024; 5:e645. [PMID: 39156766 PMCID: PMC11329757 DOI: 10.1002/mco2.645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 08/20/2024] Open
Abstract
Gene therapy has witnessed substantial advancements in recent years, becoming a constructive tactic for treating various human diseases. This review presents a comprehensive overview of these developments, with a focus on their diverse applications in different disease contexts. It explores the evolution of gene delivery systems, encompassing viral (like adeno-associated virus; AAV) and nonviral approaches, and evaluates their inherent strengths and limitations. Moreover, the review delves into the progress made in targeting specific tissues and cell types, spanning the eye, liver, muscles, and central nervous system, among others, using these gene technologies. This targeted approach is crucial in addressing a broad spectrum of genetic disorders, such as inherited lysosomal storage diseases, neurodegenerative disorders, and cardiovascular diseases. Recent clinical trials and successful outcomes in gene therapy, particularly those involving AAV and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins, are highlighted, illuminating the transformative potentials of this approach in disease treatment. The review summarizes the current status of gene therapy, its prospects, and its capacity to significantly ameliorate patient outcomes and quality of life. By offering comprehensive analysis, this review provides invaluable insights for researchers, clinicians, and stakeholders, enriching the ongoing discourse on the trajectory of disease treatment.
Collapse
Affiliation(s)
- Fanfei Liu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
| | - Ruiting Li
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Zilin Zhu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yang Yang
- Department of OphthalmologyWest China HospitalChengduSichuanChina
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Fang Lu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
| |
Collapse
|
223
|
Celik S, Yilmaz G, Akyuz S, Ozel AE. Shedding light into the biological activity of aminopterin, via molecular structural, docking, and molecular dynamics analyses. J Biomol Struct Dyn 2024; 42:7773-7794. [PMID: 37565332 DOI: 10.1080/07391102.2023.2245493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, αIIBβ3 and α5β1integrins, human dihydrofolate reductase, main protease (Mpro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), αIIBβ3 and α5β1 integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), Mpro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sefa Celik
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
| | - Gozde Yilmaz
- Opticianry Program, Vocational School, Istanbul Kultur University, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Istanbul, Turkey
| | - Aysen E Ozel
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
| |
Collapse
|
224
|
Cadet J, Angelov D, Di Mascio P, Wagner JR. Contribution of oxidation reactions to photo-induced damage to cellular DNA. Photochem Photobiol 2024; 100:1157-1185. [PMID: 38970297 DOI: 10.1111/php.13990] [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: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/08/2024]
Abstract
This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.
Collapse
Affiliation(s)
- Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LMBC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University, Balçova, Izmir, Turkey
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
225
|
Iqbal MS, Clode PL, Malik AI, Erskine W, Kotula L. Salt tolerance in mungbean is associated with controlling Na and Cl transport across roots, regulating Na and Cl accumulation in chloroplasts and maintaining high K in root and leaf mesophyll cells. PLANT, CELL & ENVIRONMENT 2024; 47:3638-3653. [PMID: 38757412 DOI: 10.1111/pce.14943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
Salinity tolerance requires coordinated responses encompassing salt exclusion in roots and tissue/cellular compartmentation of salt in leaves. We investigated the possible control points for salt ions transport in roots and tissue tolerance to Na+ and Cl- in leaves of two contrasting mungbean genotypes, salt-tolerant Jade AU and salt-sensitive BARI Mung-6, grown in nonsaline and saline (75 mM NaCl) soil. Cryo-SEM X-ray microanalysis was used to determine concentrations of Na, Cl, K, Ca, Mg, P, and S in various cell types in roots related to the development of apoplastic barriers, and in leaves related to photosynthetic performance. Jade AU exhibited superior salt exclusion by accumulating higher [Na] in the inner cortex, endodermis, and pericycle with reduced [Na] in xylem vessels and accumulating [Cl] in cortical cell vacuoles compared to BARI Mung-6. Jade AU maintained higher [K] in root cells than BARI Mung-6. In leaves, Jade AU maintained lower [Na] and [Cl] in chloroplasts and preferentially accumulated [K] in mesophyll cells than BARI Mung-6, resulting in higher photosynthetic efficiency. Salinity tolerance in Jade AU was associated with shoot Na and Cl exclusion, effective regulation of Na and Cl accumulation in chloroplasts, and maintenance of high K in root and leaf mesophyll cells.
Collapse
Affiliation(s)
- Md Shahin Iqbal
- Center for Plant Genetics and Breeding, The UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- Pulses Research Center, Bangladesh Agricultural Research Institute, Ishurdi, Bangladesh
| | - Peta L Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia, Australia
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Al Imran Malik
- Center for Plant Genetics and Breeding, The UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- International Center for Tropical Agriculture (CIAT-Asia), Lao People's Democratic Republic Office, Vientiane, Laos
| | - William Erskine
- Center for Plant Genetics and Breeding, The UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Lukasz Kotula
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
226
|
Neupane K, Narayan A, Sen Mojumdar S, Adhikari G, Garen CR, Woodside MT. Direct observation of prion-like propagation of protein misfolding templated by pathogenic mutants. Nat Chem Biol 2024; 20:1220-1226. [PMID: 39009686 DOI: 10.1038/s41589-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/06/2024] [Indexed: 07/17/2024]
Abstract
Many neurodegenerative diseases feature misfolded proteins that propagate via templated conversion of natively folded molecules. However, crucial questions about how such prion-like conversion occurs and what drives it remain unsolved, partly because technical challenges have prevented direct observation of conversion for any protein. We observed prion-like conversion in single molecules of superoxide dismutase-1 (SOD1), whose misfolding is linked to amyotrophic lateral sclerosis. Tethering pathogenic misfolded SOD1 mutants to wild-type molecules held in optical tweezers, we found that the mutants vastly increased misfolding of the wild-type molecule, inducing multiple misfolded isoforms. Crucially, the pattern of misfolding was the same in the mutant and converted wild-type domains and varied when the misfolded mutant was changed, reflecting the templating effect expected for prion-like conversion. Ensemble measurements showed decreased enzymatic activity in tethered heterodimers as conversion progressed, mirroring the single-molecule results. Antibodies sensitive to disease-specific epitopes bound to the converted protein, implying that conversion produced disease-relevant misfolded conformers.
Collapse
Affiliation(s)
- Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Abhishek Narayan
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Supratik Sen Mojumdar
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, India
| | - Gaurav Adhikari
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Craig R Garen
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
227
|
Gotthard G, Mous S, Weinert T, Maia RNA, James D, Dworkowski F, Gashi D, Furrer A, Ozerov D, Panepucci E, Wang M, Schertler GFX, Heberle J, Standfuss J, Nogly P. Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography. IUCRJ 2024; 11:792-808. [PMID: 39037420 PMCID: PMC11364019 DOI: 10.1107/s2052252524005608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 07/23/2024]
Abstract
Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
Collapse
Affiliation(s)
- Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Raiza Nara Antonelli Maia
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light SourcePaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Laboratory of Femtochemistry, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dmitry Ozerov
- Science ITPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Department of BiologyETH Zürich8093ZürichSwitzerland
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University in Kraków30-387KrakówPoland
| |
Collapse
|
228
|
Arakawa T, Tomioka Y, Akuta T, Shiraki K. The contrasting roles of co-solvents in protein formulations and food products. Biophys Chem 2024; 312:107282. [PMID: 38944944 DOI: 10.1016/j.bpc.2024.107282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Protein aggregation is a major hurdle in developing biopharmaceuticals, in particular protein formulation area, but plays a pivotal role in food products. Co-solvents are used to suppress protein aggregation in pharmaceutical proteins. On the contrary, aggregation is encouraged in the process of food product making. Thus, it is expected that co-solvents play a contrasting role in biopharmaceutical formulation and food products. Here, we show several examples that utilize co-solvents, e.g., salting-out salts, sugars, polyols and divalent cations in promoting protein-protein interactions. The mechanisms of co-solvent effects on protein aggregation and solubility have been studied on aqueous protein solution and applied to develop pharmaceutical formulation based on the acquired scientific knowledge. On the contrary, co-solvents have been used in food industries based on empirical basis. Here, we will review the mechanisms of co-solvent effects on protein-protein interactions that can be applied to both pharmaceutical and food industries and hope to convey knowledge acquired through research on co-solvent interactions in aqueous protein solution and formulation to those involved in food science and provide those involved in protein solution research with the observations on aggregation behavior of food proteins.
Collapse
Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130, USA.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd, 3333-26, Aza-Asayama, Kamitezuna Tahahagi, Ibaraki 318-0004, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd, 3333-26, Aza-Asayama, Kamitezuna Tahahagi, Ibaraki 318-0004, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| |
Collapse
|
229
|
Keil E, Lokstein H, Cogdell R, Hauer J, Zigmantas D, Thyrhaug E. Light harvesting in purple bacteria does not rely on resonance fine-tuning in peripheral antenna complexes. PHOTOSYNTHESIS RESEARCH 2024; 161:191-201. [PMID: 38907135 PMCID: PMC11324704 DOI: 10.1007/s11120-024-01107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
The ring-like peripheral light-harvesting complex 2 (LH2) expressed by many phototrophic purple bacteria is a popular model system in biological light-harvesting research due to its robustness, small size, and known crystal structure. Furthermore, the availability of structural variants with distinct electronic structures and optical properties has made this group of light harvesters an attractive testing ground for studies of structure-function relationships in biological systems. LH2 is one of several pigment-protein complexes for which a link between functionality and effects such as excitonic coherence and vibronic coupling has been proposed. While a direct connection has not yet been demonstrated, many such interactions are highly sensitive to resonance conditions, and a dependence of intra-complex dynamics on detailed electronic structure might be expected. To gauge the sensitivity of energy-level structure and relaxation dynamics to naturally occurring structural changes, we compare the photo-induced dynamics in two structurally distinct LH2 variants. Using polarization-controlled 2D electronic spectroscopy at cryogenic temperatures, we directly access information on dynamic and static disorder in the complexes. The simultaneous optimal spectral and temporal resolution of these experiments further allows us to characterize the ultrafast energy relaxation, including exciton transport within the complexes. Despite the variations in PPC molecular structure manifesting as clear differences in electronic structure and disorder, the energy-transport and-relaxation dynamics remain remarkably similar. This indicates that the light-harvesting functionality of purple bacteria within a single LH2 complex is highly robust to structural perturbations and likely does not rely on finely tuned electronic- or electron-vibrational resonance conditions.
Collapse
Affiliation(s)
- Erika Keil
- TUM School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
| | - Richard Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Room 402 Davidson Building, Glasgow, G12 8QQ, Scotland
| | - Jürgen Hauer
- TUM School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Donatas Zigmantas
- Chemical Physics, Lund University, Naturvetarvägen 16, 22362, Lund, Sweden
| | - Erling Thyrhaug
- TUM School of Natural Sciences, Department of Chemistry and Catalysis Research Center, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
| |
Collapse
|
230
|
Khoroshkin M, Asarnow D, Zhou S, Navickas A, Winters A, Goudreau J, Zhou SK, Yu J, Palka C, Fish L, Borah A, Yousefi K, Carpenter C, Ansel KM, Cheng Y, Gilbert LA, Goodarzi H. A systematic search for RNA structural switches across the human transcriptome. Nat Methods 2024; 21:1634-1645. [PMID: 39014073 PMCID: PMC11399106 DOI: 10.1038/s41592-024-02335-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/29/2024] [Indexed: 07/18/2024]
Abstract
RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3' untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.
Collapse
Affiliation(s)
- Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Asarnow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Shaopu Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institut Curie, UMR3348 CNRS, U1278 Inserm, Orsay, France
| | - Aidan Winters
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Biological and Medical Informatics, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Jackson Goudreau
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Simon K Zhou
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Christina Palka
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ashir Borah
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kian Yousefi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Carpenter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
| |
Collapse
|
231
|
Yuan Y, Dong X, Wang H, Gai F. Capturing the illusive ring-shaped intermediates in A β42 amyloid formation. BIOPHYSICS REVIEWS 2024; 5:032104. [PMID: 39359326 PMCID: PMC11444734 DOI: 10.1063/5.0222349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/16/2024] [Indexed: 10/04/2024]
Abstract
Protein/peptide amyloid fibril formation is associated with various neurodegenerative diseases and, hence, has been the subject of extensive studies. From a structure-evolution point of view, we now know a great deal about the initial and final states of this process; however, we know very little about its intermediate states. Herein, we employ liquid-phase transmission electron microscopy to directly visualize the formation of one of the intermediates formed during the aggregation process of an amyloid-forming peptide. As shown in figure, we find that Aβ42, the amyloid formation of which has been linked to the development of Alzheimer's disease, can populate a ring-shaped intermediate structure with a diameter of tens of nanometers; additionally, the air-liquid interface can "catalyze" the formation of amyloid fibrils.
Collapse
Affiliation(s)
- Yu Yuan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaozhe Dong
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Huan Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
232
|
Nagagaki Y, Kozakura Y, Mahandaran T, Fumoto Y, Nakato R, Shirahige K, Ishikawa F. Histone H3.3 chaperone HIRA renders stress-responsive genes poised for prospective lethal stresses in acquired tolerance. Genes Cells 2024; 29:722-734. [PMID: 38977420 PMCID: PMC11447927 DOI: 10.1111/gtc.13140] [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: 04/11/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress-responsive genes, including HSP70, by depositing histone H3.3 following low-dose stresses. These genes are also marked with histone H3 Lys-4 trimethylation and H3 Lys-9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.
Collapse
Affiliation(s)
- Yoshikazu Nagagaki
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuji Kozakura
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Theventhiran Mahandaran
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yukiko Fumoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryuichiro Nakato
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| |
Collapse
|
233
|
Wu H, Li Z. A new dual-thickness semi-transparent beamstop for small-angle X-ray scattering. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:1197-1208. [PMID: 39182204 PMCID: PMC11371043 DOI: 10.1107/s1600577524007392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024]
Abstract
An innovative dual-thickness semi-transparent beamstop designed to enhance the performance of small-angle X-ray scattering (SAXS) experiments is introduced. This design integrates two absorbers of differing thicknesses side by side into a single attenuator, known as a beamstop. Instead of completely stopping the direct beam, it attenuates it, allowing the SAXS detector to measure the transmitted beam through the sample. This approach achieves true synchronization in measuring both scattered and transmitted signals and effectively eliminates higher-order harmonic contributions when determining the transmission light intensity through the sample. This facilitates and optimizes signal detection and background subtraction. This contribution details the theoretical basis and practical implementation of this solution at the SAXS station on the 1W2A beamline at the Beijing Synchrotron Radiation Facility. It also anticipates its application at other SAXS stations, including that at the forthcoming High Energy Photon Source, providing an effective solution for high-precision SAXS experiments.
Collapse
Affiliation(s)
- Haijuan Wu
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
- College of Nuclear Science and TechnologyUniversity of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Zhihong Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
| |
Collapse
|
234
|
Wei X, Zhang X, Peng Y, Wu J, Mo H, An Z, Deng X, Peng Y, Liu L, Jiang W, Chen J, Hu Z, Wang Z, Zhuo L. Identification of a novel 10-hydroxyevodiamine prodrug as a potent topoisomerase inhibitor with improved aqueous solubility for treatment of hepatocellular carcinoma. Eur J Med Chem 2024; 279:116807. [PMID: 39243453 DOI: 10.1016/j.ejmech.2024.116807] [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: 05/10/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024]
Abstract
Natural product evodiamine (Evo) and its synthetic derivatives represent an attractive dual Topo 1/2 inhibitors with broad-spectrum antitumor efficacy. However, the clinical applications of these compounds have been impeded by their poor aqueous solubility. Herein, a series of water-soluble 10-substituted-N(14)-phenylevodiamine derivatives were designed and synthesized. The most potent compound 45 featuring a quaternary ammonium salt fragment achieved robust aqueous solubility and nanomolar potency against a panel of human hepatoma cell lines Huh7, HepG2, SK-Hep-1, SMMC-7721, and SMMC-7721/DOX (doxorubicin-resistant cell). Further studies revealed that 45 could inhibit Topo 1 and Topo 2, induce apoptosis, arrest the cell cycle at the G2/M stage and inhibit the migration and invasion. Compound 45 exhibited potent antitumor activity (TGI = 51.1 %, 10 mg/kg) in the Huh7 xenograft model with acceptable safety profile. In addition, a 21-day long-term dose toxicity study confirmed that the maximum tolerated dose of compound 45 was 20 mg/kg. Overall, this study presented a promising Evo-derived candidate for the treatment of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Xiuzhen Wei
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xi Zhang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yan Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Junbo Wu
- Department of Colorectal Surgery, Hengyang Central Hospital, Hengyang, Hunan, 421001, China
| | - Hanxuan Mo
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhigang An
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xinyu Deng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ying Peng
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Linyi Liu
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Weifan Jiang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jinjin Chen
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zecheng Hu
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Zhen Wang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, China; National Health Commission Key Laboratory of Birth Defect Research and Prevention Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, 410008, China; MOE Key Lab of Rare Pediatric Diseases, School of Life Sciences, Central South University, Changsha, 410000, China.
| | - Linsheng Zhuo
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| |
Collapse
|
235
|
Giubertoni G, Chagri S, Argudo PG, Prädel L, Maltseva D, Greco A, Caporaletti F, Pavan A, Ilie IM, Ren Y, Ng DYW, Bonn M, Weil T, Woutersen S. Structural adaptability and surface activity of peptides derived from tardigrade proteins. Protein Sci 2024; 33:e5135. [PMID: 39150232 PMCID: PMC11328126 DOI: 10.1002/pro.5135] [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: 03/28/2024] [Revised: 07/05/2024] [Accepted: 07/20/2024] [Indexed: 08/17/2024]
Abstract
Tardigrades are unique micro-organisms with a high tolerance to desiccation. The protection of their cells against desiccation involves tardigrade-specific proteins, which include the so-called cytoplasmic abundant heat soluble (CAHS) proteins. As a first step towards the design of peptides capable of mimicking the cytoprotective properties of CAHS proteins, we have synthesized several model peptides with sequences selected from conserved CAHS motifs and investigated to what extent they exhibit the desiccation-induced structural changes of the full-length proteins. Using circular dichroism spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations, we have found that the CAHS model peptides are mostly disordered, but adopt a moreα $$ \alpha $$ -helical structure upon addition of 2,2,2-trifluoroethanol, which mimics desiccation. This structural behavior is similar to that of full-length CAHS proteins, which also adopt more ordered conformations upon desiccation. We also have investigated the surface activity of the peptides at the air/water interface, which also mimics partial desiccation. Interestingly, sum-frequency generation spectroscopy shows that all model peptides are surface active and adopt a helical structure at the air/water interface. Our results suggest that amino acids with high helix-forming propensities might contribute to the propensity of these peptides to adopt a helical structure when fully or partially dehydrated. Thus, the selected sequences retain part of the CAHS structural behavior upon desiccation, and might be used as a basis for the design of new synthetic peptide-based cryoprotective materials.
Collapse
Affiliation(s)
- Giulia Giubertoni
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Sarah Chagri
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Pablo G Argudo
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Leon Prädel
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Daria Maltseva
- Max Planck Institute for Polymer Research, Mainz, Germany
| | | | - Federico Caporaletti
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Alberto Pavan
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ioana M Ilie
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, Amsterdam, Netherlands
- Computational Soft Matter (CSM), University of Amsterdam, Amsterdam, Netherlands
| | - Yong Ren
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - David Y W Ng
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
236
|
Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
Collapse
Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
| |
Collapse
|
237
|
Rosenholm JB. Packing in multimodal crystals and particle assemblies as models for dynamic packing during spontaneous and enforced particle movement: Settling, viscosity and elasticity. Adv Colloid Interface Sci 2024; 331:103165. [PMID: 38964197 DOI: 10.1016/j.cis.2024.103165] [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: 03/26/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 07/06/2024]
Abstract
Colloid particles (CP, 10-8-10-6 m = 10-1000 nm) are used as models for atom scale processes, such as crystallization since the process is experimentally observable. Packing of atoms in crystals resemble mono-, bi-, and trimodal packing of noncharged hard spheres (particles). When the size of one particle exceeds the two others an excluded volume consisting of small particles is created around large particles. This is also the case when colloid particles are dispersed in water. The formation of an excluded volume does not require attraction forces, but it is enforced by the presence of dissolved primary (cations) and secondary (protons of surface hydroxyls) potential determining ions. The outcome is an interfacial solid-liquid charge. This excluded volume, denoted Stern layer is characterized by the surface potential and charge density. Charge neutrality is identified by point of zero charge (pHpzc and pcpzc). Outside Stern layer another excluded volume is formed of loosely bound counterions which interact with Stern layer. The extent of this diffuse layer is given by inverse Debye length and effective ζ-potential. The overall balance between attractive and repulsive energies is provided by Derjaguin-Landau-Veerwey-Overbeek (DLVO) model. Charge neutrality is identified at isoelectric point (pHiep and pciep). The dependence of viscosity and yield stress on shear rate may be modeled by von Smoluchowski's volumetric collision frequency multiplied by some total interaction energy given by DLVO model. Equilibrium and dynamic models for settling and enforced particle movement (viscosity) are presented. Both compressive yield stress (sedimentation) and cohesive energy (viscoelasticity) are characterized by power law exponents of volume fraction. The transition of disperse suspensions (sols) to spanning clusters (gels) is identified by oscillatory rheology. The slope of linear plots of logarithmic storage (G´) and loss (G") moduli against logarithm of frequency or logarithm of volume fraction provide power law exponents from the slopes. These exponents relate to percolation and fractal dimensions characterizing the particle network. Moreover, it identifies the structure formation process either as diffusion limited cluster-cluster (DLCCA) or as reaction limited cluster-cluster (RLCCA) aggregation.
Collapse
Affiliation(s)
- Jarl B Rosenholm
- Physical Chemistry, Laboratory of Molecular Science and Engineering, Aurum Åbo Akademi University, Henriksgatan 2, 20500, Åbo, Turku, Finland.
| |
Collapse
|
238
|
Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. J Struct Biol 2024; 216:108108. [PMID: 38944401 DOI: 10.1016/j.jsb.2024.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these energies, specifically a ∼ 4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope fitted with a non-standard SP-Twin lens. We also achieved a ∼ 3.2 Å resolution reconstruction of a 115 kDa asymmetric protein complex, proving Alpine's effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ∼ 3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, bringing smaller sized particles within the scope of cryo-EM.
Collapse
Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hev Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States.
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States.
| |
Collapse
|
239
|
Foos N, Florial JB, Eymery M, Sinoir J, Felisaz F, Oscarsson M, Beteva A, Bowler MW, Nurizzo D, Papp G, Soler-Lopez M, Nanao M, Basu S, McCarthy AA. In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry. IUCRJ 2024; 11:780-791. [PMID: 39008358 PMCID: PMC11364034 DOI: 10.1107/s2052252524005785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.
Collapse
Affiliation(s)
- Nicolas Foos
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Jean-Baptise Florial
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Mathias Eymery
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Jeremy Sinoir
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Franck Felisaz
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Antonia Beteva
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Matthew W. Bowler
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Didier Nurizzo
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Gergely Papp
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | | | - Max Nanao
- European Synchrotron Radiation Facility71 Avenue des Martyrs38042GrenobleFrance
| | - Shibom Basu
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| | - Andrew A. McCarthy
- European Molecular Biology LaboratoryGrenoble Outstation, 71 Avenue des Martyrs38042GrenobleFrance
| |
Collapse
|
240
|
Wagner J, Carvajal AI, Bracher A, Beck F, Wan W, Bohn S, Körner R, Baumeister W, Fernandez-Busnadiego R, Hartl FU. Visualizing chaperonin function in situ by cryo-electron tomography. Nature 2024; 633:459-464. [PMID: 39169181 PMCID: PMC11390479 DOI: 10.1038/s41586-024-07843-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding1-3. The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor GroES at their apertures. In vitro analyses of the chaperonin reaction have shown that substrate protein folds, unimpaired by aggregation, while transiently encapsulated in the GroEL central cavity by GroES4-6. To determine the functional stoichiometry of GroEL, GroES and client protein in situ, here we visualized chaperonin complexes in their natural cellular environment using cryo-electron tomography. We find that, under various growth conditions, around 55-70% of GroEL binds GroES asymmetrically on one ring, with the remainder populating symmetrical complexes. Bound substrate protein is detected on the free ring of the asymmetrical complex, defining the substrate acceptor state. In situ analysis of GroEL-GroES chambers, validated by high-resolution structures obtained in vitro, showed the presence of encapsulated substrate protein in a folded state before release into the cytosol. Based on a comprehensive quantification and conformational analysis of chaperonin complexes, we propose a GroEL-GroES reaction cycle that consists of linked asymmetrical and symmetrical subreactions mediating protein folding. Our findings illuminate the native conformational and functional chaperonin cycle directly within cells.
Collapse
Affiliation(s)
- Jonathan Wagner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Alonso I Carvajal
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - William Wan
- Vanderbilt University Center for Structural Biology, Nashville, TN, USA
| | - Stefan Bohn
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Structural Biology, Helmholtz Center Munich, Oberschleissheim, Germany
| | - Roman Körner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Ruben Fernandez-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
- Faculty of Physics, University of Göttingen, Göttingen, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
241
|
Md S, Kotta S. Advanced drug delivery technologies for postmenopausal effects. J Control Release 2024; 373:426-446. [PMID: 39038543 DOI: 10.1016/j.jconrel.2024.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Postmenopause is the 12-month absence of menstrual periods, characterized by decreased estrogen and progesterone levels, leading to physical and psychological alterations such as hot flashes, mood swings, sleep disruptions, and skin changes. Present postmenopausal treatments include hormone replacement therapy, non-hormonal drugs, lifestyle modifications, vaginal estrogen therapy, bone health treatments, and alternative therapies. Advanced drug delivery systems (ADDSs) are essential in managing postmenopausal effects (PMEs), offering targeted and controlled delivery to alleviate symptoms and improve overall health. This review emphasizes such ADDSs for addressing PMEs. Emerging trends such as artificial ovaries are also reviewed. Additionally, the prospects of technologies such as additive manufacturing (3D and 4D printing) and artificial intelligence in further tailoring therapeutic strategies against PMEs are provided.
Collapse
Affiliation(s)
- Shadab Md
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sabna Kotta
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| |
Collapse
|
242
|
Kamera S, Sharma VK, Prasad V B, Garlapati A. Identification of potential inhibitors of Mtb InhA: a pharmacoinformatics approach. J Biomol Struct Dyn 2024; 42:7957-7971. [PMID: 37526169 DOI: 10.1080/07391102.2023.2242499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
The emergence of superbugs of multi-drug resistant (MDR/RR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (Mtb) strains at a faster rate is posing a serious threat to Tuberculosis (TB) control worldwide. Mtb enoyl-acyl carrier protein reductase (InhA) is a well-established target of the front-line anti-TB prodrug Isoniazid (INH), which requires activation by Catalase-peroxidase enzyme (KatG) in order to inhibit InhA enzyme, that is crucial for the biosynthesis of the mycobacterial cell wall. Currently, due to widespread resistance to this drug, it is necessary to identify new clinical candidates that directly inhibit InhA enzyme and do not require activation by KatG, thereby circumventing most of the resistance mechanisms. In the present study, high-throughput virtual screening of ASINEX database was carried out to identify potential direct inhibitors of Mtb InhA. Best twenty compounds with good binding energies ranging between -12.36 and -9.27 kcal/mol were selected as promising virtual screening hits. These molecules were subjected to ADME study followed by toxicity prediction. Finally, four top-ranked molecules which are structurally diverse and possess best binding affinity than the co-crystalized ligand have been chosen for MD simulation studies followed by MM-GBSA analysis to validate and ensure the stability of hits in the active site of the enzyme. Based on the 100 ns MD simulation studies and binding free energy estimates, three hit molecules B244, B369, and B310 could be considered as potential inhibitors for Mtb InhA, which are likely to be potent against INH-resistant Mtb strains after successful experimental validation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sreelatha Kamera
- Medicinal Chemistry Division, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana, India
| | - Vishnu Kumar Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Bharatam Prasad V
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Achaiah Garlapati
- Medicinal Chemistry Division, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana, India
| |
Collapse
|
243
|
Nagy G, Hoffmann SV, Jones NC, Grubmüller H. Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. APPLIED SPECTROSCOPY 2024; 78:897-911. [PMID: 38646777 DOI: 10.1177/00037028241239977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.
Collapse
Affiliation(s)
- Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| |
Collapse
|
244
|
Singh G, Al-Fahad D, Al-Zrkani MK, Chaudhuri TK, Soni H, Tandon S, Narasimhaji CV, Azam F, Patil R. Identification of potential inhibitors of HER2 targeting breast cancer-a structure-based drug design approach. J Biomol Struct Dyn 2024; 42:8184-8201. [PMID: 37565730 DOI: 10.1080/07391102.2023.2246576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Breast cancer is one of the most prevalent and malignant cancers in women. Most breast cancer patients show overexpression of the HER2 protein. The current study focused on identifying potent inhibitors of HER2 using a structure-based drug design approach. Prefiltered compounds from the Drugbank and the ZINC database were docked on HER2 protein using the FlexX docking tool of LeadIT. The docking study identified the 12 best molecules that interacted strongly with the active site of HER2 and also fulfilled the ADMET parameters. The complexes of these compounds with HER2 were further subjected to molecular dynamics simulation using GROMACS 2021.4, followed by the end-state MMGBSA binding energy calculations. The RMSD analysis was conducted to study the conformational changes, which revealed stability throughout the 100 ns simulation period. The local flexibility and dynamics of the simulated ligand-protein complexes were studied using RMSF analysis. The values of the radius of gyration were computed to analyze the compactness of HER2. The MMGBSA analysis provided insights into the energetic aspects of the system. The compound DB15187 emerged as the most potent candidate, showing MMGBSA-computed binding energy of -63.60 ± 3.39 kcal/mol. The study could help develop targeted therapies for HER2-positive breast cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gagandeep Singh
- Section of Microbiology and Chemistry, Central Ayurveda Research Institute Jhansi, CCRAS, Ministry of Ayush, India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Dhurgham Al-Fahad
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Thi-Qar, Nasiriyah, Iraq
| | - Mrtatha K Al-Zrkani
- Department of Animal Production, College of Agriculture, Wasit University, Wasit, Iraq
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Hemant Soni
- Section of Microbiology and Chemistry, Central Ayurveda Research Institute Jhansi, CCRAS, Ministry of Ayush, India
| | - Smriti Tandon
- Section of Microbiology and Chemistry, Central Ayurveda Research Institute Jhansi, CCRAS, Ministry of Ayush, India
| | | | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Rajesh Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Pune, India
| |
Collapse
|
245
|
Martínez-Torres AM, Morán J. Aquaporin 4 and the endocannabinoid system: a potential therapeutic target in brain injury. Exp Brain Res 2024; 242:2041-2058. [PMID: 39043897 PMCID: PMC11306651 DOI: 10.1007/s00221-024-06896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024]
Abstract
Brain edema is a critical complication arising from stroke and traumatic brain injury (TBI) with an important impact on patient recovery and can lead to long-term consequences. Therapeutic options to reduce edema progression are limited with variable patient outcomes. Aquaporin 4 (AQP4) is a water channel that allows bidirectional water diffusion across the astrocyte membrane and participates in the distinct phases of cerebral edema. The absence or inhibition of this channel has been demonstrated to ameliorate edema and brain damage. The endocannabinoid system (ECS) is a neuromodulator system with a wide expression in the brain and its activation has shown neuroprotective properties in diverse models of neuronal damage. This review describes and discusses the major features of ECS and AQP4 and their role during brain damage, observing that ECS stimulation reduces edema and injury size in diverse models of brain damage, however, the relationship between AQP4 expression and dynamics and ECS activation remains unclear. The research on these topics holds promising therapeutic implications for the treatment of brain edema following stroke and TBI.
Collapse
Affiliation(s)
- Ari Misael Martínez-Torres
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Apartado Postal 70-253, 04510, Ciudad de Mexico, México
| | - Julio Morán
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Apartado Postal 70-253, 04510, Ciudad de Mexico, México.
| |
Collapse
|
246
|
Sharmin S, Islam MZ, Yamazaki M. Relationship between oligoarginine-induced membrane damage of single Escherichia coli cells and entry of the peptide into the cytoplasm. Biochem Biophys Rep 2024; 39:101777. [PMID: 39091698 PMCID: PMC11292251 DOI: 10.1016/j.bbrep.2024.101777] [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: 04/28/2024] [Revised: 06/20/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024] Open
Abstract
Cell-penetrating peptides (CPPs) can enter the cytosol of eukaryotic cells without killing them whereas some CPPs exhibit antimicrobial activity against bacterial cells. Here, to elucidate the mode of interaction of the CPP nona-arginine (R9) with bacterial cells, we investigated the interactions of lissamine rhodamine B red-labeled peptide (Rh-R9) with single Escherichia coli cells encapsulating calcein using confocal laser scanning microscopy. After Rh-R9 induced the leakage of a large amount of calcein, the fluorescence intensity of the cytosol due to Rh-R9 greatly increased, indicating that Rh-R9 induces cell membrane damage, thus allowing entry of a significant amount of Rh-R9 into the cytosol. To determine if the lipid bilayer region of the membrane is the main target of Rh-R9, we then investigated the interaction of Rh-R9 with single giant unilamellar vesicles (GUVs) comprising an E. coli polar lipid extract containing small GUVs and AlexaFluor 647 hydrazide (AF647) in the lumen. Rh-R9 entered the GUV lumen without inducing AF647 leakage, but leakage eventually did occur, indicating that GUV membrane damage was induced after the entry of Rh-R9 into the GUV lumen. The Rh-R9 peptide concentration dependence of the fraction of entry of Rh-R9 after a specific interaction time was similar to that of the fraction of leaking GUVs. These results indicate that Rh-R9 can damage the lipid bilayer region of a cell membrane, which may be related to its antimicrobial activity.
Collapse
Affiliation(s)
- Sabrina Sharmin
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Md. Zahidul Islam
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka, 422-8529, Japan
- Dept. of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Masahito Yamazaki
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
- Nanomaterials Research Division, Research Institute of Electronics, Shizuoka, 422-8529, Japan
- Dept. of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| |
Collapse
|
247
|
Deng J, Zhang W, Zhang L, Qin C, Wang H, Ling W. Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review. ENVIRONMENT INTERNATIONAL 2024; 191:108972. [PMID: 39180776 DOI: 10.1016/j.envint.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.
Collapse
Affiliation(s)
- Jibao Deng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenkang Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyu Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
248
|
Onal G, Yalçın-Çakmaklı G, Özçelik CE, Boussaad I, Şeker UÖŞ, Fernandes HJR, Demir H, Krüger R, Elibol B, Dökmeci S, Salman MM. Variant-specific effects of GBA1 mutations on dopaminergic neuron proteostasis. J Neurochem 2024; 168:2543-2560. [PMID: 38641924 DOI: 10.1111/jnc.16114] [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: 10/31/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
Glucocerebrosidase 1 (GBA1) mutations are the most important genetic risk factors for Parkinson's disease (PD). Clinically, mild (e.g., p.N370S) and severe (e.g., p.L444P and p.D409H) GBA1 mutations have different PD phenotypes, with differences in age at disease onset, progression, and the severity of motor and non-motor symptoms. We hypothesize that GBA1 mutations cause the accumulation of α-synuclein by affecting the cross-talk between cellular protein degradation mechanisms, leading to neurodegeneration. Accordingly, we tested whether mild and severe GBA1 mutations differentially affect the degradation of α-synuclein via the ubiquitin-proteasome system (UPS), chaperone-mediated autophagy (CMA), and macroautophagy and differentially cause accumulation and/or release of α-synuclein. Our results demonstrate that endoplasmic reticulum (ER) stress and total ubiquitination rates were significantly increased in cells with severe GBA1 mutations. CMA was found to be defective in induced pluripotent stem cell (iPSC)-derived dopaminergic neurons with mild GBA1 mutations, but not in those with severe GBA1 mutations. When examining macroautophagy, we observed reduced formation of autophagosomes in cells with the N370S and D409H GBA1 mutations and impairments in autophagosome-lysosome fusion in cells with the L444P GBA1 mutation. Accordingly, severe GBA1 mutations were found to trigger the accumulation and release of oligomeric α-synuclein in iPSC-derived dopaminergic neurons, primarily as a result of increased ER stress and defective macroautophagy, while mild GBA1 mutations affected CMA, which is mainly responsible for the degradation of the monomeric form of α-synuclein. Overall, our findings provide new insight into the molecular basis of the clinical variability in PD associated with different GBA1 mutations.
Collapse
Affiliation(s)
- G Onal
- Department of Physiology, Anatomy and Genetics, Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - G Yalçın-Çakmaklı
- Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - C E Özçelik
- National Nanotechnology Research Center, UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - I Boussaad
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - U Ö Ş Şeker
- Interdisciplinary Neuroscience Program, National Nanotechnology Research Center, UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Hugo J R Fernandes
- Department of Physiology, Anatomy and Genetics, Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - H Demir
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - R Krüger
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
| | - B Elibol
- Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - S Dökmeci
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - M M Salman
- Department of Physiology, Anatomy and Genetics, Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| |
Collapse
|
249
|
Kumawat RL, Jena MK, Mittal S, Pathak B. Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401112. [PMID: 38716623 DOI: 10.1002/smll.202401112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/05/2024] [Indexed: 10/04/2024]
Abstract
DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.
Collapse
Affiliation(s)
- Rameshwar L Kumawat
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| |
Collapse
|
250
|
Kang N, Kim EA, Park A, Heo SY, Heo JH, Lee WK, Ryu YK, Heo SJ. Antiviral Activity of Chlorophyll Extracts from Tetraselmis sp., a Marine Microalga, Against Zika Virus Infection. Mar Drugs 2024; 22:397. [PMID: 39330278 PMCID: PMC11433109 DOI: 10.3390/md22090397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/24/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024] Open
Abstract
Recent advancements in the large-scale cultivation of Tetraselmis sp. in Korea have enabled year-round production of this marine microalgae. This study explores the potential industrial applications of Tetraselmis sp. biomass by investigating the antiviral properties of its extracts and primary components. The antiviral effects of Tetraselmis sp. extracts were evaluated in Zika virus (ZIKV)-infected cells. Following extensive isolation and purification, the main compounds were characterized using liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) analyses. Their antiviral activities were confirmed using in vitro and in silico tests. Tetraselmis sp. extracts reduced infectious viral particles and non-structural protein 1 messenger RNA levels in ZIKV-infected cells without inducing cytotoxicity. Additionally, they modulated the interferon-mediated immune system responses. Tetraselmis sp. extracts are composed of four main chlorophylls: chlorophyll a, chlorin e6-131-152-dimethyl-173-phytyl ester, hydroxychlorophyll a, and hydroxypheophytin a. Among them, chlorophyll a, chlorin e6-131-152-dimethyl-173-phytyl ester, and hydroxypheophytin showed the antiviral activities in ZIKV-infected cells and molecular docking simulations predicted interactions between these chlorophylls and ZIKV. Our findings suggest that Tetraselmis sp. chlorophyll extracts exert antiviral effects against ZIKV and could serve as potential therapeutic candidates against ZIKV infection.
Collapse
Affiliation(s)
- Nalae Kang
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Eun-A Kim
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Areumi Park
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Seong-Yeong Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Jun-Ho Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Won-Kyu Lee
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Yong-Kyun Ryu
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
| | - Soo-Jin Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (A.P.); (S.-Y.H.); (J.-H.H.); (W.-K.L.); (Y.-K.R.)
- Department of Biology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| |
Collapse
|