Dynamic behavior of biomaterials uncovered by cryo-electron microscopy.

2020 ◽  
Vol 23 ◽  
Author(s):  
Yimin Zhao ◽  
Yizhen Zhao ◽  
Bingquan Peng ◽  
Lei Zhang
Keyword(s):  
Electron Microscopy ◽  
Protein Interactions ◽  
Rapid Development ◽  
Conformational Space ◽  
Biological Macromolecules ◽  
Protein Protein Interactions ◽  
Static Structure ◽  
Cryo Electron Microscopy ◽  
Biological Complexes ◽  
Functional Mechanisms

: Structural biology develops rapidly as time goes on. Based only on static structure analysis of biomaterials is not enough to satisfy the studies of their functional mechanisms, with a huge obstacle for the dynamic process of biological complexes. The rapid development of cryo-electron microscopy(cryo-EM) technology makes that it is possible to observe the near-atomic resolution structures and dynamic nature of biological macromolecules, in the fields of dynamic characteristics of proteins, protein-protein interactions, molecular recognition, and structure-based design. In this review, we systematically elaborate the contribution of cryo-EM technology in the field of biomaterials such as ribosome motion, membrane protein structure and conformational space, dynamic transmission within the plasma membrane and clinical applications. We also put forwards a new standpoint in the development of cryo-EM technology.

scholarly journals The endurance of flash-frozen biologics can be improved allowing high-resolution electron microscopy tomography on individual proteins

2021 ◽  
Author(s):  
Andrea Fera
Keyword(s):  
Electron Microscopy ◽  
Protein Interactions ◽  
Electron Beams ◽  
High Resolution Electron Microscopy ◽  
High Energy ◽  
Experimental Session ◽  
Protein Protein Interactions ◽  
Viral Origin ◽  
Cryo Electron Microscopy ◽  
Resolution Electron

Abstract Here surprising results are shown demonstrating a workflow possibly able to exploit the discreet nature of interactions between high-energy electron beams and matter. Isolated protein constructs have been imaged after an original temperature-curing in vacuum, introduced recently for flash-frozen rigid biopolymers, and here applied to flash-frozen oligomers of viral origin. These results, if confirmed, may extend to plastics and bio-oligomers the access to atomic coordinates in one experimental session, when imaged by electron microscopy. Which is the case when imaging semiconductors or other solid materials, provided that the samples are not damaged by the interaction with accelerated electron beams in vacuum. Therefore, potentially, this workflow introduces the possibility of achieving atomic resolution in only one experiment with data only about one individual protein, maybe out of thermodynamic equilibrium. Such data are vital to understand protein-protein interactions. Finally, this workflow offers the possibility, new to cryo-electron microscopy samples, to store a sample indefinitely under liquid nitrogen for imaging the same molecules in more than one experimental session.

scholarly journals Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher R. Horne ◽  
Hariprasad Venugopal ◽  
Santosh Panjikar ◽  
David M. Wood ◽  
Amy Henrickson ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Dna Binding ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nutrient Source ◽  
Cryo Electron Microscopy ◽  
Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

scholarly journals Unravelling biological macromolecules with cryo-electron microscopy

Nature ◽  
2016 ◽  
Vol 537 (7620) ◽  
pp. 339-346 ◽  
Author(s):  
Rafael Fernandez-Leiro ◽  
Sjors H. W. Scheres
Keyword(s):  
Electron Microscopy ◽  
Biological Macromolecules ◽  
Cryo Electron Microscopy

High-throughput proteomics and the fight against pathogens

2016 ◽  
Vol 12 (8) ◽  
pp. 2373-2384 ◽  
Author(s):  
Anita Horvatić ◽  
Josipa Kuleš ◽  
Nicolas Guillemin ◽  
Asier Galan ◽  
Vladimir Mrljak ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Animal Welfare ◽  
High Throughput ◽  
Protein Interactions ◽  
Rapid Development ◽  
Protein Protein Interactions ◽  
Major Threat ◽  
Host Pathogen ◽  
Pathogen Protein

Pathogens pose a major threat to human and animal welfare. Understanding the interspecies host–pathogen protein–protein interactions could lead to the development of novel strategies to combat infectious diseases through the rapid development of new therapeutics.

scholarly journals Structure of PDE3A–SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jie Chen ◽  
Nan Liu ◽  
Yinpin Huang ◽  
Yuanxun Wang ◽  
Yuxing Sun ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Catalytic Domain ◽  
Cultured Cells ◽  
Hydrophobic Interactions ◽  
Complex Structure ◽  
Protein A ◽  
Protein Translation ◽  
Protein Protein Interactions ◽  
Cryo Electron Microscopy ◽  
Apoptosis Inducer

AbstractMolecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-β-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (SLFN12). They do so by binding to the PDE3A enzymatic pocket that allows the compound-bound PDE3A to recruit and stabilize SLFN12, which in turn blocks protein translation, leading to apoptosis. In this work, we report the high-resolution cryo-electron microscopy structure of PDE3A-SLFN12 complexes isolated from cultured HeLa cells pre-treated with either anagrelide, or nauclefine, or DNMDP. The PDE3A-SLFN12 complexes exhibit a butterfly-like shape, forming a heterotetramer with these small molecules, which are packed in a shallow pocket in the catalytic domain of PDE3A. The resulting small molecule-modified interface binds to the short helix (E552-I558) of SLFN12 through hydrophobic interactions, thus “gluing” the two proteins together. Based on the complex structure, we designed and synthesized analogs of anagrelide, a known drug used for the treatment of thrombocytosis, to enhance their interactions with SLFN12, and achieved superior efficacy in inducing apoptosis in cultured cells as well as in tumor xenografts.

Fluorescence resonance energy transfer in revealing protein–protein interactions in living cells

2021 ◽  
Author(s):  
Sukesh R. Bhaumik
Keyword(s):  
Single Cell ◽  
Protein Interactions ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Living Cells ◽  
Biological Processes ◽  
Protein Protein Interactions ◽  
Functional Mechanisms

Genes are expressed to proteins for a wide variety of fundamental biological processes at the cellular and organismal levels. However, a protein rarely functions alone, but rather acts through interactions with other proteins to maintain normal cellular and organismal functions. Therefore, it is important to analyze the protein–protein interactions to determine functional mechanisms of proteins, which can also guide to develop therapeutic targets for treatment of diseases caused by altered protein–protein interactions leading to cellular/organismal dysfunctions. There is a large number of methodologies to study protein interactions in vitro, in vivo and in silico, which led to the development of many protein interaction databases, and thus, have enriched our knowledge about protein–protein interactions and functions. However, many of these interactions were identified in vitro, but need to be verified/validated in living cells. Furthermore, it is unclear whether these interactions are direct or mediated via other proteins. Moreover, these interactions are representative of cell- and time-average, but not a single cell in real time. Therefore, it is crucial to detect direct protein–protein interactions in a single cell during biological processes in vivo, towards understanding the functional mechanisms of proteins in living cells. Importantly, a fluorescence resonance energy transfer (FRET)-based methodology has emerged as a powerful technique to decipher direct protein–protein interactions at a single cell resolution in living cells, which is briefly described in a limited available space in this mini-review.

scholarly journals A WAVELET BASED ALTERNATIVE ITERATION METHOD FOR THE ORIENTATION REFINEMENT OF CRYO-ELECTRON MICROSCOPY 3D RECONSTRUCTION

2015 ◽  
Vol 20 (3) ◽  
pp. 396-408 ◽  
Author(s):  
Zhucui Jing ◽  
Ming Li
Keyword(s):  
Electron Microscopy ◽  
Iteration Method ◽  
Three Dimensional ◽  
Particle Method ◽  
Biological Macromolecules ◽  
Orthonormal Bases ◽  
Cryo Electron Microscopy ◽  
Marquardt Algorithm ◽  
Density Map ◽  
Particle Images

Cryo-electron microscopy (cryo-EM) single particle method (SPM) reconstructs the three-dimensional (3D) density map of biological macromolecules using 2D particle images with estimated orientations. The estimated orientations have errors which result in the decrease in resolution of the reconstructed map. We propose a wavelet orthonormal bases based iteration method by refining alternatively the orientations and the map using Levenberg–Marquardt algorithm and soft-thresholding, respectively. The convergence analysis of the proposed algorithm is provided and numerical experiments for simulated particle images show its good performance.

scholarly journals Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis

2021 ◽  
Author(s):  
Yang Zhang ◽  
Tianyuan Liu ◽  
Jing Wang ◽  
Bohao Zou ◽  
Le Li ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Intercellular Communication ◽  
Rapid Development ◽  
Cell Communication ◽  
Supplementary Information ◽  
Protein Protein Interactions ◽  
Communication Analysis ◽  
Mediate Cell ◽  
Intercellular Communications ◽  
Cell Cell

Abstract Motivation Ligand–receptor (L–R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L–R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L–R interactions in order to study the functional effects of cell–cell communications would be of great value. Results In this study, we developed Cellinker, a platform of literature-supported L–R interactions that play roles in cell–cell communication. We aimed to provide a useful platform for studies on cell–cell communication mediated by L–R interactions. The current version of Cellinker documents over 3700 human and 3200 mouse L–R protein–protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L–R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16L–R PPIs involved in CoV–human interactions (including 12L–R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L–R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies. Availability and implementation Cellinker is available at http://www.rna-society.org/cellinker/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation

2017 ◽  
Author(s):  
Kyle A. Barlow ◽  
Shane O Conchúir ◽  
Samuel Thompson ◽  
Pooja Suresh ◽  
James E. Lucas ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Energy Function ◽  
Large Scale ◽  
Additive Model ◽  
Conformational Space ◽  
Side Chain ◽  
Free Energies ◽  
Protein Protein Interactions ◽  
Conformational Plasticity ◽  
Macromolecular Modeling

AbstractComputationally modeling changes in binding free energies upon mutation (interface ΔΔG) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using “backrub” to generate an ensemble of models, then applying torsion minimization, side chain repacking and averaging across this ensemble to estimate interface ΔΔG values. We tested our method on a curated benchmark set of 1240 mutants, and found the method outperformed existing methods that sampled conformational space to a lesser degree. We observed considerable improvements with flex ddG over existing methods on the subset of small side chain to large side chain mutations, as well as for multiple simultaneous non-alanine mutations, stabilizing mutations, and mutations in antibody-antigen interfaces. Finally, we applied a generalized additive model (GAM) approach to the Rosetta energy function; the resulting non-linear reweighting model improved agreement with experimentally determined interface DDG values, but also highlights the necessity of future energy function improvements.

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