1
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Ems-McClung SC, Cassity M, Prasannajith A, Walczak CE. The Kinesin-14 tail: Dual microtubule binding domains drive spindle morphogenesis through tight microtubule cross-linking and robust sliding. Mol Biol Cell 2025; 36:ar72. [PMID: 40327372 DOI: 10.1091/mbc.e25-02-0083] [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: 05/07/2025] Open
Abstract
Proper spindle assembly requires the Kinesin-14 (K-14) family of motors to organize microtubules (MT) into the bipolar spindle by cross-linking and sliding antiparallel and parallel MTs through their motor and tail domains. How they mediate these different activities is unclear. We identified two MT-binding domains (MBD1 and MBD2) within the Xenopus K-14 XCTK2 tail and found that MBD1 MT affinity was weaker than MBD2. Comparable with full-length GFP-XCTK2 wild-type protein (GX-WT), GFP-XCTK2 containing the MBD1 mutations (GX-MBD1mut) stimulated spindle assembly, localized moderately on the spindle, and formed narrow spindles. In contrast, GX-MBD2mut only partially stimulated spindle assembly, localized weakly on the spindle, and formed shorter spindles. Biochemical reconstitution of MT cross-linking and sliding demonstrated that GX-MBD2mut slid antiparallel MTs faster than GX-WT and GX-MBD1mut. However, GX-WT and GX-MBD1mut statically cross-linked the majority of parallel MTs, whereas GX-MBD2mut equally slid and statically cross-linked parallel MTs without affecting their sliding velocity. These results provide a mechanism by which the two different MBDs in the K-14 tail balance antiparallel MT sliding velocity (MBD1) and tight parallel MT cross-linking (MBD2), which are important for spindle assembly and localization, and provide a basis for characterizing how molecular motors organize MTs within the spindle.
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2
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Sonani RR, Bianco S, Kreutzberger MAB, Adams DJ, Egelman EH. Cryo-EM for atomic characterization of supramolecular gels. Faraday Discuss 2025. [PMID: 40365900 PMCID: PMC12076579 DOI: 10.1039/d4fd00181h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 12/16/2024] [Indexed: 05/15/2025]
Abstract
While there have been great advances in the design and synthesis of supramolecular gels, their characterization methods have largely stayed the same, with electron microscopy of dried samples, or small-angle scattering and spectroscopy dominating the approaches used. Although these methods provide valuable insights into structural properties, they are unable to unambiguously generate reliable atomic models that can further guide the site-specific modification of supramolecular gelators. Cryogenic electron microscopy (cryo-EM), allowing the high-resolution imaging of the sample in a hydrated state, has emerged as the dominant technique in structural biology, but has yet to become a routine method in materials science. Here, we describe the use of cryo-EM to determine the atomic structure of the tubular micelle formed by the dipeptide CarbIF, revealing the mechanism of assembly and gelation. Using the CarbIF micelle as an example, we highlight some of the challenges in using cryo-EM to study such materials, and how determination of the helical symmetry can be the most difficult aspect of such a project.
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Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Simona Bianco
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Dave J Adams
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
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3
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Böken D, Wu Y, Zhang Z, Klenerman D. Detecting the Undetectable: Advances in Methods for Identifying Small Tau Aggregates in Neurodegenerative Diseases. Chembiochem 2025; 26:e202400877. [PMID: 39688878 PMCID: PMC12002113 DOI: 10.1002/cbic.202400877] [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: 10/23/2024] [Revised: 12/16/2024] [Accepted: 12/17/2024] [Indexed: 12/18/2024]
Abstract
Tau, a microtubule-associated protein, plays a critical role in maintaining neuronal structure and function. However, in neurodegenerative diseases such as Alzheimer's disease and other tauopathies, tau misfolds and aggregates into oligomers and fibrils, leading to neuronal damage. Tau oligomers are increasingly recognised as the most neurotoxic species, inducing synaptic dysfunction and contributing to disease progression. Detecting these early-stage aggregates is challenging due to their low concentration and high heterogeneity in biological samples. Traditional methods such as immunostaining and enzyme-linked immunosorbent assay (ELISA) lack the sensitivity and specificity to reliably detect small tau aggregates. Advanced single-molecule approaches, including single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule pull-down (SiMPull), offer improved sensitivity for studying tau aggregation at the molecular level. These emerging tools provide critical insights into tau pathology, enabling earlier detection and characterisation of disease-relevant aggregates, thereby offering potential for the development of targeted therapies and diagnostic approaches for tauopathies.
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Affiliation(s)
- Dorothea Böken
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0AHUK
| | - Yunzhao Wu
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0AHUK
| | - Ziwei Zhang
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0AHUK
| | - David Klenerman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0AHUK
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4
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Ems-McClung SC, Cassity M, Prasannajith A, Walczak CE. The Kinesin-14 Tail: Dual microtubule binding domains drive spindle morphogenesis through tight microtubule cross-linking and robust sliding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.25.640188. [PMID: 40060502 PMCID: PMC11888285 DOI: 10.1101/2025.02.25.640188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2025]
Abstract
Proper spindle assembly requires the Kinesin-14 family of motors to organize microtubules (MTs) into the bipolar spindle by cross-linking and sliding anti-parallel and parallel MTs through their motor and tail domains. How they mediate these different activities is unclear. We identified two MT binding domains (MBD1 and MBD2) within the Xenopus Kinesin-14 XCTK2 tail and found that MBD1 MT affinity was weaker than MBD2. Comparable to full-length GFP-XCTK2 wild-type protein (GX-WT), GFP-XCTK2 containing the MBD1 mutations (GX-MBD1mut) stimulated spindle assembly, localized moderately on the spindle, and formed narrow spindles. In contrast, GX-MBD2mut only partially stimulated spindle assembly, localized weakly on the spindle, and formed shorter spindles. Biochemical reconstitution of MT cross-linking and sliding demonstrated that GX-MBD2mut slid anti-parallel MTs faster than GX-WT and GX-MBD1mut. However, GX-WT and GX-MBD1mut statically cross-linked the majority of parallel MTs, whereas GX-MBD2mut equally slid and statically cross-linked parallel MTs without affecting their sliding velocity. These results provide a mechanism by which the two different MT binding domains in the Kinesin-14 tail balance anti-parallel MT sliding velocity (MBD1) and tight parallel MT cross-linking (MBD2), which are important for spindle assembly and localization, and provide a basis for characterizing how molecular motors organize MTs within the spindle.
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5
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Xin D, Kurien L, Briggs K, Schimek A, Dambra R, Hochdorfer D, Arnouk TA, Brgles M, Gautam S, Hotter D, Solzin J, Kriehuber T, Ashour J, Vigil A, Hawley M, He X. Characterization of VSV-GP morphology by cryo-EM imaging and SEC-MALS. Mol Ther Methods Clin Dev 2025; 33:101429. [PMID: 40083959 PMCID: PMC11904549 DOI: 10.1016/j.omtm.2025.101429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 02/03/2025] [Indexed: 03/16/2025]
Abstract
Vesicular stomatitis virus expressing the glycoprotein of the lymphocytic choriomeningitis virus (VSV-GP) is a promising platform for oncolytic viruses and cancer vaccines. In this work, cryoelectron microscopy (cryo-EM) imaging was employed to directly visualize VSV-GP particles. Several different subpopulations of virus particle morphology were observed. Definition and fraction counting of subpopulations enabled quantitative comparison of subpopulation profiles between several VSV-GP samples. In developing an orthogonal method with higher throughput, we showed that the morphological profile of the VSV-GP particles can be characterized by size exclusion chromatography coupled with a multi-angle light scattering detector (SEC-MALS) based on a novel shape-based separation mechanism. Together, the two complementary techniques enable the analysis of morphological profile for VSV-GP and potentially other non-spherical viruses or nanoparticles.
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Affiliation(s)
- Dongyue Xin
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Leela Kurien
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Katherine Briggs
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | | | - Richard Dambra
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Daniel Hochdorfer
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tanja A. Arnouk
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Marija Brgles
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Saurabh Gautam
- ViraTherapeutics GmbH, Innsbruck, Austria
- Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - Dominik Hotter
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Johannes Solzin
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Kriehuber
- Viral Therapeutics Center, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Joseph Ashour
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Adam Vigil
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Michael Hawley
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Xiaorong He
- Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
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6
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Beggs KW, Dougherty TE, Kassab AJ, Giannuzzi LA. Heat Transfer Analysis of Cryogenic EXLO Specimen Handling. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2025; 31:ozae121. [PMID: 39804714 DOI: 10.1093/mam/ozae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 10/17/2024] [Accepted: 11/14/2024] [Indexed: 01/16/2025]
Abstract
A conduction heat transfer analysis of ex situ lift-out specimen handling under cryogenic conditions (cryo-EXLO) is performed and compared with experimentally determined temperature values using a type K thermocouple. Using a finite-volume solver for heat conduction, the analysis confirms that manipulation of a specimen by a probe above a working surface cooled at liquid nitrogen (LN2) temperatures can remain below the critical vitreous temperature up to several hundreds of micrometers above the working surface, allowing for ample distance for lift out and specimen manipulation. In addition, the temperature above the cryogenic shuttle sample holder working surface remains below the vitreous temperature for several tens of minutes without adding cryogen, yielding sufficient time to complete multiple manipulations. Periodically topping off the cryogen level may allow for unlimited cryo-EXLO manipulations with this hardware and geometry.
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Affiliation(s)
- Kyle W Beggs
- Centecorp LLC, Longwood, 147 Parsons Rd, FL 32779, USA
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7
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Montserrat-Canals M, Cordara G, Krengel U. Allostery. Q Rev Biophys 2025; 58:e5. [PMID: 39849666 DOI: 10.1017/s0033583524000209] [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: 01/25/2025]
Abstract
Allostery describes the ability of biological macromolecules to transmit signals spatially through the molecule from an allosteric site – a site that is distinct from orthosteric binding sites of primary, endogenous ligands – to the functional or active site. This review starts with a historical overview and a description of the classical example of allostery – hemoglobin – and other well-known examples (aspartate transcarbamoylase, Lac repressor, kinases, G-protein-coupled receptors, adenosine triphosphate synthase, and chaperonin). We then discuss fringe examples of allostery, including intrinsically disordered proteins and inter-enzyme allostery, and the influence of dynamics, entropy, and conformational ensembles and landscapes on allosteric mechanisms, to capture the essence of the field. Thereafter, we give an overview over central methods for investigating molecular mechanisms, covering experimental techniques as well as simulations and artificial intelligence (AI)-based methods. We conclude with a review of allostery-based drug discovery, with its challenges and opportunities: with the recent advent of AI-based methods, allosteric compounds are set to revolutionize drug discovery and medical treatments.
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Affiliation(s)
- Mateu Montserrat-Canals
- Department of Chemistry, University of Oslo, Oslo, Norway
- Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, Oslo, Norway
- Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Oslo, Norway
- Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
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8
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Caspy I, Wang Z, Bharat TA. Structural biology inside multicellular specimens using electron cryotomography. Q Rev Biophys 2025; 58:e6. [PMID: 39801355 PMCID: PMC7617309 DOI: 10.1017/s0033583525000010] [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: 01/23/2025]
Abstract
The electron cryomicroscopy (cryo-EM) resolution revolution has shifted structural biology into a new era, enabling the routine structure determination of macromolecular complexes at an unprecedented rate. Building on this, electron cryotomography (cryo-ET) offers the potential to visualise the native three-dimensional organisation of biological specimens, from cells to tissues and even entire organisms. Despite this huge potential, the study of tissue-like multicellular specimens via cryo-ET still presents numerous challenges, wherein many steps in the workflow are being developed or in urgent need of improvement. In this review, we outline the latest techniques currently utilised for in situ imaging of multicellular specimens, while clearly enumerating their associated limitations. We consider every step in typical workflows employed by various laboratories, including sample preparation, data collection and image analysis, to highlight recent progress and showcase prominent success stories. By considering the entire structural biology workflow for multicellular specimens, we identify which future exciting developments in hardware and software could enable comprehensive in situ structural biology investigations, bringing forth a new age of discovery in molecular structural and cell biology.
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Affiliation(s)
- Ido Caspy
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Zhexin Wang
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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9
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Hong R, Alagbe BD, Mattei A, Sheikh AY, Tuckerman ME. Enhanced and Efficient Predictions of Dynamic Ionization through Constant-pH Adiabatic Free Energy Dynamics. J Chem Theory Comput 2024; 20:10010-10021. [PMID: 39513519 PMCID: PMC11603612 DOI: 10.1021/acs.jctc.4c00704] [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: 05/31/2024] [Revised: 10/14/2024] [Accepted: 10/16/2024] [Indexed: 11/15/2024]
Abstract
Dynamic or structurally induced ionization is a critical aspect of many physical, chemical, and biological processes. Molecular dynamics (MD) based simulation approaches, specifically constant pH MD methods, have been developed to simulate ionization states of molecules or proteins under experimentally or physiologically relevant conditions. While such approaches are now widely utilized to predict ionization sites of macromolecules or to study physical or biological phenomena, they are often computationally expensive and require long simulation times to converge. In this article, using the principles of adiabatic free energy dynamics, we introduce an efficient technique for performing constant pH MD simulations within the framework of the adiabatic free energy dynamics (AFED) approach. We call the new approach pH-AFED. We show that pH-AFED provides highly accurate predictions of protein residue pKa values, with a MUE of 0.5 pKa units when coupled with driven adiabatic free energy dynamics (d-AFED), while reducing the required simulation times by more than an order of magnitude. In addition, pH-AFED can be easily integrated into most constant pH MD codes or implementations and flexibly adapted to work in conjunction with enhanced sampling algorithms that target collective variables. We demonstrate that our approaches, with both pH-AFED standalone as well as pH-AFED combined with collective variable based enhanced sampling, provide promising predictive accuracy, with a MUE of 0.6 and 0.5 pKa units respectively, on a diverse range of proteins and enzymes, ranging up to 186 residues and 21 titratable sites. Lastly, we demonstrate how this approach can be utilized to understand the in vivo performance engineered antibodies for immunotherapy.
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Affiliation(s)
- Richard
S. Hong
- AbbVie
Inc., Molecular Profiling and Drug Delivery, Research & Development, 1 N Waukegan Road, North Chicago, Illinois 60064, United States
- Department
of Chemistry, New York University, New York City, New York 10003, United States
| | - Busayo D. Alagbe
- AbbVie
Inc., Molecular Profiling and Drug Delivery, Research & Development, 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- AbbVie
Inc., Molecular Profiling and Drug Delivery, Research & Development, 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Ahmad Y. Sheikh
- AbbVie
Inc., Molecular Profiling and Drug Delivery, Research & Development, 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Mark E. Tuckerman
- Department
of Chemistry, New York University, New York City, New York 10003, United States
- Courant
Institute of Mathematical Sciences, New
York University, New York, New York 10012, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
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10
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Mohammad Karim A. Principles and Biomedical Applications of Self-Assembled Peptides: Potential Treatment of Type 2 Diabetes Mellitus. Pharmaceutics 2024; 16:1442. [PMID: 39598565 PMCID: PMC11597675 DOI: 10.3390/pharmaceutics16111442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 11/08/2024] [Accepted: 11/10/2024] [Indexed: 11/29/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) is the most prevalent metabolic disorder worldwide. There have been tremendous efforts to find a safe and prolonged effective therapy for its treatment. Peptide hormones, from certain organisms in the human body, as the pharmaceutical agents, have shown outstanding profiles of efficacy and safety in plasma glucose regulation. Their therapeutic promises have undergone intensive investigations via examining their physicochemical and pharmacokinetic properties. Their major drawback is their short half-life in vivo. To address this challenge, researchers have recently started to apply the state-of-the-art molecular self-assembly on peptide hormones to form nanofibrillar structures, as a smart nanotherapeutic drug delivery technique, to tremendously enhance their prolonged bioactivity in vivo. This revolutionary therapeutic approach would significantly improve patient compliance. First, this review provides a comprehensive summary on the pathophysiology of T2DM, various efforts to treat this chronic disorder, and the limitations and drawbacks of these treatment approaches. Next, this review lays out detailed insights on various aspects of peptide self-assembly: adverse effects, potential applications in nanobiotechnology, thermodynamics and kinetics of the process, as well as the molecular structures of the self-assembled configurations. Furthermore, this review elucidates the recent efforts on applying reversible human-derived peptide self-assembly to generate highly organized smart nanostructured drug formulations known as nanofibrils to regulate and prolong the bioactivity of the human gut hormone peptides in vivo to treat T2DM. Finally, this review highlights the future research directions to advance the knowledge on the state-of-the-art peptide self-assembly process to apply the revolutionary smart nanotherapeutics for treatment of chronic disorders such as T2DM with highly improved patient compliance.
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Affiliation(s)
- Alireza Mohammad Karim
- Nanoscience Centre, Department of Engineering, University of Cambridge, 11 J. J. Thomson Avenue, Cambridge CB3 0FF, UK
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11
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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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12
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Glaser A, Chandrashekar J, Vasquez S, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Hooper M, Liddell A, Rohde J, Hellevik A, Takasaki K, Erion Barner L, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Tasic B, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1×1×3 μm optical resolution over a large field of view (10.6×8.0 mm 2 ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.
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13
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Joshi B, de Lannoy C, Howarth MR, Kim SH, Joo C. iMAX FRET (Information Maximized FRET) for Multipoint Single-Molecule Structural Analysis. NANO LETTERS 2024; 24:8487-8494. [PMID: 38975639 PMCID: PMC11261617 DOI: 10.1021/acs.nanolett.4c00447] [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: 01/26/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Understanding the structure of biomolecules is vital for deciphering their roles in biological systems. Single-molecule techniques have emerged as alternatives to conventional ensemble structure analysis methods for uncovering new biology in molecular dynamics and interaction studies, yet only limited structural information could be obtained experimentally. Here, we address this challenge by introducing iMAX FRET, a one-pot method that allows ab initio 3D profiling of individual molecules using two-color FRET measurements. Through the stochastic exchange of fluorescent weak binders, iMAX FRET simultaneously assesses multiple distances on a biomolecule within a few minutes, which can then be used to reconstruct the coordinates of up to four points in each molecule, allowing structure-based inference. We demonstrate the 3D reconstruction of DNA nanostructures, protein quaternary structures, and conformational changes in proteins. With iMAX FRET, we provide a powerful approach to advance the understanding of biomolecular structure by expanding conventional FRET analysis to three dimensions.
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Affiliation(s)
- Bhagyashree
S. Joshi
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Carlos de Lannoy
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Mark R. Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Sung Hyun Kim
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
- Department
of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
- New
and Renewable Energy Research Center, Ewha
Womans University, Seoul 03760, Republic
of Korea
| | - Chirlmin Joo
- Kavli
Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft 2629HZ, The Netherlands
- Department
of Physics, Ewha Womans University, Seoul 03760, Republic of Korea
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14
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Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. J Struct Biol 2024; 216:108072. [PMID: 38431179 PMCID: PMC11162944 DOI: 10.1016/j.jsb.2024.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/11/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
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Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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15
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Khoshouei A, Kempf G, Mykhailiuk V, Griessing JM, Honemann MN, Kater L, Cavadini S, Dietz H. Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM. NANO LETTERS 2024; 24. [PMID: 38602296 PMCID: PMC11057029 DOI: 10.1021/acs.nanolett.4c00915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024]
Abstract
DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse scientific and technological applications due to its ability to integrate various molecular functionalities in a programmable manner. In this study, we examined the impact of internal crossover distribution and the compositional uniformity of staple strands on the structure of multilayer DNA origami using cryogenic electron microscopy (cryo-EM) single-particle analysis. A refined DNA object was utilized as an alignment framework in a host-guest model, where we successfully resolved an 8 kDa thrombin binding aptamer (TBA) linked to the host object. Our results broaden the spectrum of DNA in structural applications.
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Affiliation(s)
- Ali Khoshouei
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Georg Kempf
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Volodymyr Mykhailiuk
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Johanna Mariko Griessing
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Maximilian Nicolas Honemann
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Lukas Kater
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich
Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Hendrik Dietz
- Laboratory
for Biomolecular Nanotechnology, Department of Biosciences, School
of Natural Sciences, Technical University
of Munich, Am Coulombwall 4a, 85748 Garching, Germany
- Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
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16
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Strickland MR, Rau MJ, Summers B, Basore K, Wulf J, Jiang H, Chen Y, Ulrich JD, Randolph GJ, Zhang R, Fitzpatrick JAJ, Cashikar AG, Holtzman DM. Apolipoprotein E secreted by astrocytes forms antiparallel dimers in discoidal lipoproteins. Neuron 2024; 112:1100-1109.e5. [PMID: 38266643 PMCID: PMC10994765 DOI: 10.1016/j.neuron.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Apolipoprotein E gene (APOE) is of great interest due to its role as a risk factor for late-onset Alzheimer's disease. ApoE is secreted by astrocytes in the central nervous system in high-density lipoprotein (HDL)-like lipoproteins. Structural models of lipidated ApoE of high resolution could aid in a mechanistic understanding of how ApoE functions in health and disease. Using monoclonal Fab and F(ab')2 fragments, we characterize the structure of lipidated ApoE on astrocyte-secreted lipoproteins. Our results provide support for the "double-belt" model of ApoE in nascent discoidal HDL-like lipoproteins, where two ApoE proteins wrap around the nanodisc in an antiparallel conformation. We further show that lipidated, recombinant ApoE accurately models astrocyte-secreted ApoE lipoproteins. Cryogenic electron microscopy of recombinant lipidated ApoE further supports ApoE adopting antiparallel dimers in nascent discoidal lipoproteins.
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Affiliation(s)
| | - Michael J Rau
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - John Wulf
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Hong Jiang
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Yun Chen
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Department of Pathology and Immunology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Jason D Ulrich
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Knight Alzheimer's Disease Research Center, 4488 Forest Park Ave., St. Louis, MO 63108, USA
| | - Gwendalyn J Randolph
- Department of Pathology and Immunology, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Anil G Cashikar
- Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Department of Psychiatry, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Taylor Family institute for Innovative Psychiatric Research, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - David M Holtzman
- Department of Neurology, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Knight Alzheimer's Disease Research Center, 4488 Forest Park Ave., St. Louis, MO 63108, USA.
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17
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Wang L, Zimanyi CM. Cryo-EM sample preparation for high-resolution structure studies. Acta Crystallogr F Struct Biol Commun 2024; 80:74-81. [PMID: 38530656 PMCID: PMC11058511 DOI: 10.1107/s2053230x24002553] [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: 01/13/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. In this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.
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Affiliation(s)
- Liguo Wang
- Laboratory for BioMolecular Structure, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Christina M. Zimanyi
- National Center for CryoEM Access and Training, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
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18
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Zuke JD, Burton BM. From isotopically labeled DNA to fluorescently labeled dynamic pili: building a mechanistic model of DNA transport to the cytoplasmic membrane. Microbiol Mol Biol Rev 2024; 88:e0012523. [PMID: 38466096 PMCID: PMC10966944 DOI: 10.1128/mmbr.00125-23] [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: 03/12/2024] Open
Abstract
SUMMARYNatural competence, the physiological state wherein bacteria produce proteins that mediate extracellular DNA transport into the cytosol and the subsequent recombination of DNA into the genome, is conserved across the bacterial domain. DNA must successfully translocate across formidable permeability barriers during import, including the cell membrane(s) and the cell wall, that are normally impermeable to large DNA polymers. This review will examine the mechanisms underlying DNA transport from the extracellular space to the cytoplasmic membrane. First, the challenges inherent to DNA movement through the cell periphery will be discussed to provide context for DNA transport during natural competence. The following sections will trace the development of a comprehensive model for DNA translocation to the cytoplasmic membrane, highlighting the crucial studies performed over the last century that have contributed to building contemporary DNA import models. Finally, this review will conclude by reflecting on what is still unknown about the process and the possible solutions to overcome these limitations.
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Affiliation(s)
- Jason D. Zuke
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Briana M. Burton
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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19
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Beggs KW, Kassab AJ, Colletta M, Yu Y, Kourkoutis LF, Darwish AA, Giannuzzi LA. Conjugate Multimode Heat Transfer Analysis of Cryogenic EXLO Manipulation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:66-76. [PMID: 38180779 DOI: 10.1093/micmic/ozad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
In this study, a conjugate radiation/conduction multimode heat transfer analysis of cryogenic focused ion beam (FIB) milling steps necessary for producing ex situ lift out specimens under cryogenic conditions (cryo-EXLO) is performed. Using finite volume for transient heat conduction and enclosure theory for radiation heat transfer, the analysis shows that as long as the specimen is attached or touching the FIB side wall trenches, the specimen will remain vitreous indefinitely, while actively cooled at liquid nitrogen (LN2) temperatures. To simulate the time needed to perform a transfer step to move the bulk sample containing the FIB-thinned specimen from the cryo-FIB to the cryo-EXLO cryostat, the LN2 temperature active cooling is turned off after steady-state conditions are reached and the specimen is monitored over time until the critical devitrification temperature is reached. Under these conditions, the sample will remain vitreous for >3 min, which is more than enough time needed to perform the cryo-transfer step from the FIB to the cryostat, which takes only ∼10 s. Cryo-transmission electron microscopy images of a manipulated cryo-EXLO yeast specimen prepared with cryo-FIB corroborates the heat transfer analysis.
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Affiliation(s)
- Kyle W Beggs
- Centecorp LLC, 147 Parsons Rd, Longwood, FL 32779, USA
| | | | - Michael Colletta
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Yue Yu
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Lena F Kourkoutis
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Physical Sciences Building, Cornell University, Ithaca, NY, USA
| | - Ahmed A Darwish
- EXpressLO LLC, 5483 Lee St, Unit 12, Lehigh Acres, FL 33971, USA
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20
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [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: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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21
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Smith MD, Darryl Quarles L, Demerdash O, Smith JC. Drugging the entire human proteome: Are we there yet? Drug Discov Today 2024; 29:103891. [PMID: 38246414 DOI: 10.1016/j.drudis.2024.103891] [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: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Each of the ∼20,000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). We compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.
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Affiliation(s)
- Micholas Dean Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - L Darryl Quarles
- Departments of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; ORRxD LLC, 3404 Olney Drive, Durham, NC 27705, USA
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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22
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Shein M, Hitzenberger M, Cheng TC, Rout SR, Leitl KD, Sato Y, Zacharias M, Sakata E, Schütz AK. Characterizing ATP processing by the AAA+ protein p97 at the atomic level. Nat Chem 2024; 16:363-372. [PMID: 38326645 PMCID: PMC10914628 DOI: 10.1038/s41557-024-01440-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
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Affiliation(s)
- Mikhail Shein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manuel Hitzenberger
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Tat Cheung Cheng
- Institute for Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
| | - Smruti R Rout
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
| | - Kira D Leitl
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany
- Bavarian NMR Center, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Germany.
| | - Eri Sakata
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany.
- Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany.
| | - Anne K Schütz
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, München, Germany.
- Bavarian NMR Center, Technical University of Munich, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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23
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Xu D, Ando N. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570849. [PMID: 38405773 PMCID: PMC10888874 DOI: 10.1101/2023.12.08.570849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models that have been proven successful in many computer vision tasks, and have been previously applied to cryo-EM micrograph filtering. In this work, we demonstrate that two strategies, fine-tuning models from pretrained weights and including the power spectrum of micrographs as input, can greatly improve the attainable prediction accuracy of CNN models. The resulting software package, Miffi, is open-source and freely available for public use (https://github.com/ando-lab/miffi).
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Affiliation(s)
- Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
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24
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Guo Z, Liu J, Wang Y, Chen M, Wang D, Xu D, Cheng J. Diffusion models in bioinformatics and computational biology. NATURE REVIEWS BIOENGINEERING 2024; 2:136-154. [PMID: 38576453 PMCID: PMC10994218 DOI: 10.1038/s44222-023-00114-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 04/06/2024]
Abstract
Denoising diffusion models embody a type of generative artificial intelligence that can be applied in computer vision, natural language processing and bioinformatics. In this Review, we introduce the key concepts and theoretical foundations of three diffusion modelling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks and score stochastic differential equations). We then explore their applications in bioinformatics and computational biology, including protein design and generation, drug and small-molecule design, protein-ligand interaction modelling, cryo-electron microscopy image data analysis and single-cell data analysis. Finally, we highlight open-source diffusion model tools and consider the future applications of diffusion models in bioinformatics.
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Affiliation(s)
- Zhiye Guo
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Jian Liu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Yanli Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Mengrui Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, USA
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25
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Castón JR, Luque D. Conventional Electron Microscopy, Cryogenic Electron Microscopy, and Cryogenic Electron Tomography of Viruses. Subcell Biochem 2024; 105:81-134. [PMID: 39738945 DOI: 10.1007/978-3-031-65187-8_3] [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] [Indexed: 01/02/2025]
Abstract
Electron microscopy (EM) techniques have been crucial for understanding the structure of biological specimens such as cells, tissues and macromolecular assemblies. Viruses and related viral assemblies are ideal targets for structural studies that help to define essential biological functions. Whereas conventional EM methods use chemical fixation, dehydration, and staining of the specimens, cryogenic electron microscopy (cryo-EM) preserves the native hydrated state. Combined with image processing and three-dimensional reconstruction techniques, cryo-EM provides three-dimensional maps of these macromolecular complexes from projection images, at atomic or near-atomic resolutions. Cryo-EM is also a major technique in structural biology for dynamic studies of functional complexes, which are often unstable, flexible, scarce, or transient in their native environments. State-of-the-art techniques in structural virology now extend beyond purified symmetric capsids and focus on the asymmetric elements such as the packaged genome and minor structural proteins that were previously missed. As a tool, cryo-EM also complements high-resolution techniques such as X-ray diffraction and NMR spectroscopy; these synergistic hybrid approaches provide important new information. Three-dimensional cryogenic electron tomography (cryo-ET), a variation of cryo-EM, goes further, and allows the study of pleomorphic and complex viruses not only in their physiological state but also in their natural environment in the cell, thereby bridging structural studies at the molecular and cellular levels. Cryo-EM and cryo-ET have been applied successfully in basic research, shedding light on fundamental aspects of virus biology and providing insights into threatening viruses, including SARS-CoV-2, responsible for the COVID-19 pandemic.
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Affiliation(s)
- José R Castón
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Madrid, Spain.
| | - Daniel Luque
- School of Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia.
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, Australia.
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26
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Deniaud A, Kabasakal BV, Bufton JC, Schaffitzel C. Sample Preparation for Electron Cryo-Microscopy of Macromolecular Machines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:173-190. [PMID: 38507207 DOI: 10.1007/978-3-031-52193-5_12] [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: 03/22/2024]
Abstract
High-resolution structure determination by electron cryo-microscopy underwent a step change in recent years. This now allows study of challenging samples which previously were inaccessible for structure determination, including membrane proteins. These developments shift the focus in the field to the next bottlenecks which are high-quality sample preparations. While the amounts of sample required for cryo-EM are relatively small, sample quality is the key challenge. Sample quality is influenced by the stability of complexes which depends on buffer composition, inherent flexibility of the sample, and the method of solubilization from the membrane for membrane proteins. It further depends on the choice of sample support, grid pre-treatment and cryo-grid freezing protocol. Here, we discuss various widely applicable approaches to improve sample quality for structural analysis by cryo-EM.
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Affiliation(s)
- Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG - Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Burak V Kabasakal
- School of Biochemistry, University of Bristol, Bristol, UK
- Turkish Accelerator and Radiation Laboratory, Gölbaşı, Ankara, Türkiye
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27
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Vallejo DD, Corstvet JL, Fernández FM. Triboelectric Nanogenerators: Low-Cost Power Supplies for Improved Electrospray Ionization. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117167. [PMID: 38053979 PMCID: PMC10695355 DOI: 10.1016/j.ijms.2023.117167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Electrospray ionization (ESI) is one of the most popular methods to generate ions for mass spectrometry (MS). When compared with other ionization techniques, it can generate ions from liquid-phase samples without additives, retaining covalent and non-covalent interactions of the molecules of interest. When hyphenated to liquid chromatography, it greatly expands the versatility of MS analysis of complex mixtures. However, despite the extensive growth in the application of ESI, the technique still suffers from some drawbacks when powered by direct current (DC) power supplies. Triboelectric nanogenerators promise to be a new power source for the generation of ions by ESI, improving on the analytical capabilities of traditional DC ESI. In this review we highlight the fundamentals of ESI driven by DC power supplies, its contrasting qualities to triboelectric nanogenerator power supplies, and its applications to three distinct fields of research: forensics, metabolomics, and protein structure analysis.
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Affiliation(s)
- Daniel D. Vallejo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joseph L. Corstvet
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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28
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Poinsignon T, Gallopin M, Grognet P, Malagnac F, Lelandais G, Poulain P. 3D models of fungal chromosomes to enhance visual integration of omics data. NAR Genom Bioinform 2023; 5:lqad104. [PMID: 38058589 PMCID: PMC10696920 DOI: 10.1093/nargab/lqad104] [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: 06/09/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in Saccharomyces cerevisiae, the backbones of the cohesin anchor regions, which were aligned all along the chromosomes, (ii) in Schizosaccharomyces pombe, the oscillations of the coiling of chromosome arms throughout the cell cycle and (iii) in Neurospora crassa, the massive relocalization of histone marks in mutants of heterochromatin regulators. 3D modeling of the chromosomes brings new opportunities for visual integration of omics data. This holistic perspective supports intuition and lays the foundation for building new concepts.
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Affiliation(s)
- Thibault Poinsignon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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29
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Bodakuntla S, Kuhn CC, Biertümpfel C, Mizuno N. Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry. Front Mol Biosci 2023; 10:1252529. [PMID: 37867557 PMCID: PMC10587472 DOI: 10.3389/fmolb.2023.1252529] [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: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.
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Affiliation(s)
- Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
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30
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Liang J, Yang X, Hu T, Gao Y, Yang Q, Yang H, Peng W, Zhou X, Guddat LW, Zhang B, Rao Z, Liu F. Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC. Structure 2023; 31:1158-1165.e3. [PMID: 37619560 DOI: 10.1016/j.str.2023.07.014] [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: 03/23/2023] [Revised: 06/25/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only trehalose import pathway in Mtb. Conformational dynamics of ABC transporters is an important feature to explain how they operate, but experimental structures are determined in a static environment. Therefore, a detailed transport mechanism cannot be elucidated because there is a lack of intermediate structures. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the Mycobacterium smegmatis (M. smegmatis) trehalose-specific importer LpqY-SugABC complex in five different conformations. These structures have been classified and reconstructed from a single cryo-EM dataset. This study allows a comprehensive understanding of the trehalose recycling mechanism in Mycobacteria and also demonstrates the potential of single-particle cryo-EM to explore the dynamic structures of other ABC transporters and molecular machines.
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Affiliation(s)
- Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Yang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Peng
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiaoting Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing, China; Laboratory of Structural Biology, Tsinghua University, Beijing, China.
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.
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31
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Yun JS, Hwangbo SA, Jeong YG. Preparation of Uniform Nano Liposomes Using Focused Ultrasonic Technology. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2618. [PMID: 37836259 PMCID: PMC10574396 DOI: 10.3390/nano13192618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
Liposomes are microspheres produced by placing phospholipids in aqueous solutions. Liposomes have the advantage of being able to encapsulate both hydrophilic and hydrophobic functional substances and are thus important mediators used in cosmetics and pharmaceuticals. It is important for liposomes to have small sizes, uniform particle size distribution, and long-term stability. Previously, liposomes have been prepared using a homo mixer, microfluidizer, and horn and bath types of sonicators. However, it is difficult to produce liposomes with small sizes and uniform particle size distribution using these methods. Therefore, we have developed a focused ultrasound method to produce nano-sized liposomes with better size control. In this study, the liposome solutions were prepared using the focused ultrasound method and conventional methods. The liposome solutions were characterized for their size distribution, stability, and morphology. Results showed that the liposome solution prepared using focused ultrasonic equipment had a uniform particle size distribution with an average size of 113.6 nm and a polydispersity index value of 0.124. Furthermore, the solution showed good stability in dynamic light scattering measurements for 4 d and Turbiscan measurements for 1 week.
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Affiliation(s)
- Ji-Soo Yun
- Nanosafety Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), 267 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea;
- Department of Applied Organic Materials Engineering, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seon-Ae Hwangbo
- Nanosafety Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), 267 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea;
| | - Young-Gyu Jeong
- Department of Applied Organic Materials Engineering, Chungnam National University, Daejeon 34134, Republic of Korea
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32
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Wu C, Guo D. Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution. Int J Mol Sci 2023; 24:14165. [PMID: 37762466 PMCID: PMC10531853 DOI: 10.3390/ijms241814165] [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: 07/09/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.
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Affiliation(s)
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
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33
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Lata K, Charles S, Mangala Prasad V. Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy. J Struct Biol 2023; 215:107993. [PMID: 37414374 DOI: 10.1016/j.jsb.2023.107993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.
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Affiliation(s)
- Kiran Lata
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sylvia Charles
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Vidya Mangala Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India; Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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34
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DiIorio MC, Kulczyk AW. Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy. MICROMACHINES 2023; 14:1674. [PMID: 37763837 PMCID: PMC10534518 DOI: 10.3390/mi14091674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. However, the inherent dynamics and structural variability of biological complexes coupled with the large number of experimental images generated by a cryo-EM experiment make data processing nontrivial. In particular, ab initio reconstruction and atomic model building remain major bottlenecks that demand substantial computational resources and manual intervention. Approaches utilizing recent innovations in artificial intelligence (AI) technology, particularly deep learning, have the potential to overcome the limitations that cannot be adequately addressed by traditional image processing approaches. Here, we review newly proposed AI-based methods for ab initio volume generation, heterogeneous 3D reconstruction, and atomic model building. We highlight the advancements made by the implementation of AI methods, as well as discuss remaining limitations and areas for future development.
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Affiliation(s)
- Megan C. DiIorio
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Biochemistry & Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
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35
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Fineberg A, Takagi Y, Thirumurugan K, Andrecka J, Billington N, Young G, Cole D, Burgess SA, Curd AP, Hammer JA, Sellers JR, Kukura P, Knight PJ. Myosin-5 varies its steps along the irregular F-actin track. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.16.549178. [PMID: 37503193 PMCID: PMC10370000 DOI: 10.1101/2023.07.16.549178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Molecular motors employ chemical energy to generate unidirectional mechanical output against a track. By contrast to the majority of macroscopic machines, they need to navigate a chaotic cellular environment, potential disorder in the track and Brownian motion. Nevertheless, decades of nanometer-precise optical studies suggest that myosin-5a, one of the prototypical molecular motors, takes uniform steps spanning 13 subunits (36 nm) along its F-actin track. Here, we use high-resolution interferometric scattering (iSCAT) microscopy to reveal that myosin takes strides spanning 22 to 34 actin subunits, despite walking straight along the helical actin filament. We show that cumulative angular disorder in F-actin accounts for the observed proportion of each stride length, akin to crossing a river on variably-spaced stepping stones. Electron microscopy revealed the structure of the stepping molecule. Our results indicate that both motor and track are soft materials that can adapt to function in complex cellular conditions.
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Affiliation(s)
- Adam Fineberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Kavitha Thirumurugan
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
- Present address: Structural Biology Lab, Pearl Research Park, SBST, Vellore Institute of Technology, Vellore-632 014, India
| | - Joanna Andrecka
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Neil Billington
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
- Present address: Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, U.S.A
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Refeyn Ltd., Unit 9, Trade City, Sandy Ln W, Littlemore, Oxford OX4 6FF, U.K
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- Present address: Refeyn Ltd., Unit 9, Trade City, Sandy Ln W, Littlemore, Oxford OX4 6FF, U.K
| | - Stan A. Burgess
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Alistair P. Curd
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - John A. Hammer
- Cell and Developmental Biology Center, NHLBI, National Institutes of Health, Bethesda, MD 20892, U.S.A
| | - James R. Sellers
- Laboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, U.K
| | - Peter J. Knight
- Astbury Centre for Structural Molecular Biology, and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
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36
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Amani K, Shivnauth V, Castroverde CDM. CBP60-DB: An AlphaFold-predicted plant kingdom-wide database of the CALMODULIN-BINDING PROTEIN 60 protein family with a novel structural clustering algorithm. PLANT DIRECT 2023; 7:e509. [PMID: 37435612 PMCID: PMC10331130 DOI: 10.1002/pld3.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CALMODULIN-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation, and diversification in most species remain unclear. Here, we have created CBP60-DB (https://cbp60db.wlu.ca/), a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs (encoding 2376 unique transcripts and 1996 unique proteins) across 62 phylogenetically diverse genomes in the plant kingdom. We have employed deep learning-predicted structural analyses using AlphaFold2 and then generated dedicated web pages for all plant CBP60 proteins. Importantly, we have generated a novel clustering visualization algorithm to interrogate kingdom-wide structural similarities for more efficient inference of conserved functions across various plant taxa. Because well-characterized CBP60 proteins in Arabidopsis are known to be transcription factors with putative calmodulin-binding domains, we have integrated external bioinformatic resources to analyze protein domains and motifs. Collectively, we present a plant kingdom-wide identification of this important protein family in a user-friendly AlphaFold-anchored database, representing a novel and significant resource for the broader plant biology community.
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Affiliation(s)
- Keaun Amani
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
| | - Vanessa Shivnauth
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
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37
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 PMCID: PMC10226581 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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38
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Durham J, Zhang J, Humphreys IR, Pei J, Cong Q. Recent advances in predicting and modeling protein-protein interactions. Trends Biochem Sci 2023; 48:527-538. [PMID: 37061423 DOI: 10.1016/j.tibs.2023.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 04/17/2023]
Abstract
Protein-protein interactions (PPIs) drive biological processes, and disruption of PPIs can cause disease. With recent breakthroughs in structure prediction and a deluge of genomic sequence data, computational methods to predict PPIs and model spatial structures of protein complexes are now approaching the accuracy of experimental approaches for permanent interactions and show promise for elucidating transient interactions. As we describe here, the key to this success is rich evolutionary information deciphered from thousands of homologous sequences that coevolve in interacting partners. This covariation signal, revealed by sophisticated statistical and machine learning (ML) algorithms, predicts physiological interactions. Accurate artificial intelligence (AI)-based modeling of protein structures promises to provide accurate 3D models of PPIs at a proteome-wide scale.
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Affiliation(s)
- Jesse Durham
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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39
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Fromm SA, O'Connor KM, Purdy M, Bhatt PR, Loughran G, Atkins JF, Jomaa A, Mattei S. The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. Nat Commun 2023; 14:1095. [PMID: 36841832 PMCID: PMC9968351 DOI: 10.1038/s41467-023-36742-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.
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Affiliation(s)
- Simon A Fromm
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Kate M O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Michael Purdy
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland. .,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA, USA. .,Centre for Cell and Membrane Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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40
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Oliva M, Gago F, Kamimura S, Díaz JF. Alternative Approaches to Understand Microtubule Cap Morphology and Function. ACS OMEGA 2023; 8:3540-3550. [PMID: 36743020 PMCID: PMC9893253 DOI: 10.1021/acsomega.2c06926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Microtubules (MTs) are essential cellular machines built from concatenated αβ-tubulin heterodimers. They are responsible for two central and opposite functions from the dynamic point of view: scaffolding (static filaments) and force generation (dynamic MTs). These roles engage multiple physiological processes, including cell shape, polarization, division and movement, and intracellular long-distance transport. At the most basic level, the MT regulation is chemical because GTP binding and hydrolysis have the ability to promote assembly and disassembly in the absence of any other constraint. Due to the stochastic GTP hydrolysis, a chemical gradient from GTP-bound to GDP-bound tubulin is created at the MT growing end (GTP cap), which is translated into a cascade of structural regulatory changes known as MT maturation. This is an area of intense research, and several models have been proposed based on information mostly gathered from macromolecular crystallography and cryo-electron microscopy studies. However, these classical structural biology methods lack temporal resolution and can be complemented, as shown in this mini-review, by other approaches such as time-resolved fiber diffraction and computational modeling. Together with studies on structurally similar tubulins from the prokaryotic world, these inputs can provide novel insights on MT assembly, dynamics, and the GTP cap.
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Affiliation(s)
- María
Ángela Oliva
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
| | - Federico Gago
- Department
of Biomedical Sciences and IQM-UAH Associate Unit, University of Alcalá, E-28805 Alcalá de Henares, Spain
| | - Shinji Kamimura
- Department
of Biological Sciences, Faculty of Science and Engineering, Chuo University, 112-8551 Tokyo, Japan
| | - J. Fernando Díaz
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
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41
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Exploring different computational approaches for effective diagnosis of breast cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:141-150. [PMID: 36509230 DOI: 10.1016/j.pbiomolbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Breast cancer has been identified as one among the top causes of female death worldwide. According to recent research, earlier detection plays an important role toward fortunate medicaments and thus, decreasing the mortality rate due to breast cancer among females. This review provides a fleeting summary involving traditional diagnostic procedures from the past and today, and also modern computational tools that have greatly aided in the identification of breast cancer. Computational techniques involving different algorithms such as Support vector machines, deep learning techniques and robotics are popular among the academicians for detection of breast cancer. They discovered that Convolutional neural network was a common option for categorization among such approaches. Deep learning techniques are evaluated using performance indicators such as accuracy, sensitivity, specificity, or measure. Furthermore, molecular docking, homology modeling and Molecular dynamics Simulation gives a road map for future discussions about developing improved early detection approaches that holds greater potential in increasing the survival rate of cancer patients. The different computational techniques can be a new dominion among researchers and combating the challenges associated with breast cancer.
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42
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Marshall NF, Mickelin O, Singer A. FAST EXPANSION INTO HARMONICS ON THE DISK: A STEERABLE BASIS WITH FAST RADIAL CONVOLUTIONS. SIAM JOURNAL ON SCIENTIFIC COMPUTING : A PUBLICATION OF THE SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2023; 45:A2431-A2457. [PMID: 39144915 PMCID: PMC11324236 DOI: 10.1137/22m1542775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
We present a fast and numerically accurate method for expanding digitized L × L images representing functions on [-1, 1]2 supported on the diskx ∈ R 2 : | x | < 1 in the harmonics (Dirichlet Laplacian eigenfunctions) on the disk. Our method, which we refer to as the Fast Disk Harmonics Transform (FDHT), runs in 𝒪 L 2 log L operations. This basis is also known as the Fourier-Bessel basis, and it has several computational advantages: it is orthogonal, ordered by frequency, and steerable in the sense that images expanded in the basis can be rotated by applying a diagonal transform to the coefficients. Moreover, we show that convolution with radial functions can also be efficiently computed by applying a diagonal transform to the coefficients.
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Affiliation(s)
| | - Oscar Mickelin
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08540 USA
| | - Amit Singer
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08540 USA
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43
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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44
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Driggers CM, Shyng SL. Mechanistic insights on KATP channel regulation from cryo-EM structures. J Gen Physiol 2022; 155:213723. [PMID: 36441147 PMCID: PMC9700523 DOI: 10.1085/jgp.202113046] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Gated by intracellular ATP and ADP, ATP-sensitive potassium (KATP) channels couple cell energetics with membrane excitability in many cell types, enabling them to control a wide range of physiological processes based on metabolic demands. The KATP channel is a complex of four potassium channel subunits from the Kir channel family, Kir6.1 or Kir6.2, and four sulfonylurea receptor subunits, SUR1, SUR2A, or SUR2B, from the ATP-binding cassette (ABC) transporter family. Dysfunction of KATP channels underlies several human diseases. The importance of these channels in human health and disease has made them attractive drug targets. How the channel subunits interact with one another and how the ligands interact with the channel to regulate channel activity have been long-standing questions in the field. In the past 5 yr, a steady stream of high-resolution KATP channel structures has been published using single-particle cryo-electron microscopy (cryo-EM). Here, we review the advances these structures bring to our understanding of channel regulation by physiological and pharmacological ligands.
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Affiliation(s)
- Camden M. Driggers
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, OR
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, OR,Correspondence to Show-Ling Shyng:
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45
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Sung MW, Driggers CM, Mostofian B, Russo JD, Patton BL, Zuckerman DM, Shyng SL. Ligand-mediated Structural Dynamics of a Mammalian Pancreatic K ATP Channel. J Mol Biol 2022; 434:167789. [PMID: 35964676 PMCID: PMC9618280 DOI: 10.1016/j.jmb.2022.167789] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
Regulation of pancreatic KATP channels involves orchestrated interactions of their subunits, Kir6.2 and SUR1, and ligands. Previously we reported KATP channel cryo-EM structures in the presence and absence of pharmacological inhibitors and ATP, focusing on the mechanisms by which inhibitors act as pharmacological chaperones of KATP channels (Martin et al., 2019). Here we analyzed the same cryo-EM datasets with a focus on channel conformational dynamics to elucidate structural correlates pertinent to ligand interactions and channel gating. We found pharmacological inhibitors and ATP enrich a channel conformation in which the Kir6.2 cytoplasmic domain is closely associated with the transmembrane domain, while depleting one where the Kir6.2 cytoplasmic domain is extended away into the cytoplasm. This conformational change remodels a network of intra- and inter-subunit interactions as well as the ATP and PIP2 binding pockets. The structures resolved key contacts between the distal N-terminus of Kir6.2 and SUR1's ABC module involving residues implicated in channel function and showed a SUR1 residue, K134, participates in PIP2 binding. Molecular dynamics simulations revealed two Kir6.2 residues, K39 and R54, that mediate both ATP and PIP2 binding, suggesting a mechanism for competitive gating by ATP and PIP2.
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Affiliation(s)
- Min Woo Sung
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA. https://twitter.com/MinWooSung5
| | - Camden M Driggers
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Barmak Mostofian
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - John D Russo
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Bruce L Patton
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, USA.
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.
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46
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Ahmed S, Chattopadhyay G, Manjunath K, Bhasin M, Singh N, Rasool M, Das S, Rana V, Khan N, Mitra D, Asok A, Singh R, Varadarajan R. Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region. Front Mol Biosci 2022; 9:997653. [PMID: 36275627 PMCID: PMC9585320 DOI: 10.3389/fmolb.2022.997653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The Mycobacterium tuberculosis genome harbours nine toxin-antitoxin (TA) systems of the mazEF family. These consist of two proteins, a toxin and an antitoxin, encoded in an operon. While the toxin has a conserved fold, the antitoxins are structurally diverse and the toxin binding region is typically intrinsically disordered before binding. We describe high throughput methodology for accurate mapping of interfacial residues and apply it to three MazEF complexes. The method involves screening one partner protein against a panel of chemically masked single cysteine mutants of its interacting partner, displayed on the surface of yeast cells. Such libraries have much lower diversity than those generated by saturation mutagenesis, simplifying library generation and data analysis. Further, because of the steric bulk of the masking reagent, labeling of virtually all exposed epitope residues should result in loss of binding, and buried residues are inaccessible to the labeling reagent. The binding residues are deciphered by probing the loss of binding to the labeled cognate partner by flow cytometry. Using this methodology, we have identified the interfacial residues for MazEF3, MazEF6 and MazEF9 TA systems of M. tuberculosis. In the case of MazEF9, where a crystal structure was available, there was excellent agreement between our predictions and the crystal structure, superior to those with AlphaFold2. We also report detailed biophysical characterization of the MazEF3 and MazEF9 TA systems and measured the relative affinities between cognate and non-cognate toxin–antitoxin partners in order to probe possible cross-talk between these systems.
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Affiliation(s)
- Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Neelam Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Mubashir Rasool
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sayan Das
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Varsha Rana
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Neha Khan
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Debarghya Mitra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- *Correspondence: Raghavan Varadarajan,
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47
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Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
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Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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48
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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49
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 PMCID: PMC9480104 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J. Piper
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M. Johnson
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M. Sexton
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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50
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Jiang H, Meng F, Lu D, Chen Y, Luo G, Chen Y, Chen J, Chen C, Zhang X, Su D. High-throughput FastCloning technology: A low-cost method for parallel cloning. PLoS One 2022; 17:e0273873. [PMID: 36084059 PMCID: PMC9462701 DOI: 10.1371/journal.pone.0273873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
FastCloning, a reliable cloning technique for plasmid construction, is a widely used protocol in biomedical research laboratories. Only two-step molecular manipulations are required to add a gene (cDNA) of interest into the desired vector. However, parallel cloning of the gene into multiple vectors is still a labor-intensive operation, which requires a range of primers for different vectors in high-throughput cloning projects. The situation could even be worse if multiple fragments of DNA are required to be added into one plasmid. Here, we describe a high-throughput FastCloning (HTFC) method, a protocol for parallel cloning by adding an adaptor sequence into all vectors. The target gene and vectors were PCR amplified separately to obtain the insert product and linear vectors with 18-base overlapping at each end of the DNAs required for FastCloning. Furthermore, a method for generating polycistronic bacterial constructs based on the same strategy as that used for HTFC was developed. Thus, the HTFC technique is a simple, effective, reliable, and low-cost tool for parallel cloning.
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Affiliation(s)
- Hua Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Fan Meng
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Deren Lu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yanjuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Guilin Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Yuejun Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
| | - Jun Chen
- Jujing-Chengdu Biotech, Chengdu, Sichuan, P.R. China
| | - Cheng Chen
- Department of Gynecology and Obstetrics, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P.R. China
| | - Xi Zhang
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, P.R. China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, P.R. China
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