scholarly journals Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms

2018 ◽  
Author(s):  
Antonio Martinez-Sanchez ◽  
Zdravko Kochovski ◽  
Ulrike Laugks ◽  
Johannes Meyer zum Alten Borgloh ◽  
Saikat Chakraborty ◽  
...  
Keyword(s):  
De Novo ◽  
Electron Tomography ◽  
Protein Complexes ◽  
3D Structure ◽  
Unsupervised Classification ◽  
Molecular Architecture ◽  
Intact Cells ◽  
Heterogeneous Membrane ◽  
Membrane Bound ◽  
Template Free

AbstractWith faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography (cryo-ET) provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification. Applying this procedure to tomograms of intact cells and isolated endoplasmic reticulum (ER), we detected and classified small protein complexes like the ER protein translocons, which were not detected by other methods before. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Therefore the procedure presented allows a comprehensive detection and a structural analysis of complexes in their native state. In addition, we present structural evidence that different ribosome-free translocon species are present at the ER membrane, determine their 3D structure, and show that they have different localization patterns forming nanodomains.

Role of cryo-ET in membrane bioenergetics research

2013 ◽  
Vol 41 (5) ◽  
pp. 1227-1234 ◽  
Author(s):  
Karen M. Davies ◽  
Bertram Daum
Keyword(s):  
Spatial Organization ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Mitochondrial Diseases ◽  
Atp Synthesis ◽  
Cellular Level ◽  
Molecular Organization ◽  
Cellular Context ◽  
Membrane Bound ◽  
The Individual

To truly understand bioenergetic processes such as ATP synthesis, membrane-bound substrate transport or flagellar rotation, systems need to be analysed in a cellular context. Cryo-ET (cryo-electron tomography) is an essential part of this process, as it is currently the only technique which can directly determine the spatial organization of proteins at the level of both the cell and the individual protein complexes. The need to assess bioenergetic processes at a cellular level is becoming more and more apparent with the increasing interest in mitochondrial diseases. In recent years, cryo-ET has contributed significantly to our understanding of the molecular organization of mitochondria and chloroplasts. The present mini-review first describes the technique of cryo-ET and then discusses its role in membrane bioenergetics specifically in chloroplasts and mitochondrial research.

scholarly journals The molecular infrastructure of glutamatergic synapses in the mammalian forebrain

2021 ◽  
Author(s):  
J. Peukes ◽  
M. Lovatt ◽  
C. Leistner ◽  
J. Boulanger ◽  
D. R. Morado ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Synaptic Cleft ◽  
Mouse Genetics ◽  
Mammalian Brain ◽  
Molecular Architecture ◽  
Glutamatergic Synapses ◽  
Synaptic Remodeling ◽  
Membrane Bound ◽  
Active Processes ◽  
Cytoskeletal Elements

AbstractGlutamatergic synapses form the vast majority of connections within neuronal circuits but how these subcellular structures are molecularly organized within the mammalian brain is poorly understood. Conventional electron microscopy using chemically fixed, metal-stained tissue has identified a proteinaceous, membrane-associated thickening called the ‘postsynaptic density’ (PSD). Here, we combined mouse genetics and cryo-electron tomography to determine the 3D molecular architecture of fresh synapses in the adult forebrain. The native glutamatergic synapse lacked a PSD. Instead, a concentrated ‘synaptoplasm’ consisting of cytoskeletal elements, macromolecular complexes and membrane-bound organelles extended throughout the pre- and post-synaptic compartments. Snapshots of active processes gave insights into the architectural basis for synaptic remodeling. Clusters of 4-60 ionotropic glutamate receptors were positioned inside and outside the synaptic cleft. Together, these information-rich tomographic maps present a detailed molecular framework for the coordinated activity within mammalian brain synapses.

scholarly journals Backbone-independent NMR resonance assignments of methyl probes in large proteins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Santrupti Nerli ◽  
Viviane S. De Paula ◽  
Andrew C. McShan ◽  
Nikolaos G. Sgourakis
Keyword(s):  
Structural Model ◽  
Isotope Labeling ◽  
De Novo ◽  
Nuclear Overhauser Effect ◽  
Protein Complexes ◽  
3D Structure ◽  
Resonance Assignments ◽  
Large Proteins ◽  
Using Data ◽  
Nuclear Overhauser

AbstractMethyl-specific isotope labeling is a powerful tool to study the structure, dynamics and interactions of large proteins and protein complexes by solution-state NMR. However, widespread applications of this methodology have been limited by challenges in obtaining confident resonance assignments. Here, we present Methyl Assignments Using Satisfiability (MAUS), leveraging Nuclear Overhauser Effect cross-peak data, peak residue type classification and a known 3D structure or structural model to provide robust resonance assignments consistent with all the experimental inputs. Using data recorded for targets with known assignments in the 10–45 kDa size range, MAUS outperforms existing methods by up to 25,000 times in speed while maintaining 100% accuracy. We derive de novo assignments for multiple Cas9 nuclease domains, demonstrating that the methyl resonances of multi-domain proteins can be assigned accurately in a matter of days, while reducing biases introduced by manual pre-processing of the raw NOE data. MAUS is available through an online web-server.

Neuroligin-2 as a central organizer of inhibitory synapses in health and disease

2020 ◽  
Vol 13 (663) ◽  
pp. eabd8379
Author(s):  
Heba Ali ◽  
Lena Marth ◽  
Dilja Krueger-Burg
Keyword(s):  
Synaptic Transmission ◽  
Synapse Formation ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Inhibitory Synapses ◽  
Molecular Architecture ◽  
Cellular Functions ◽  
Altered Expression ◽  
Health And Disease ◽  
Flow Of Information

Postsynaptic organizational protein complexes play central roles both in orchestrating synapse formation and in defining the functional properties of synaptic transmission that together shape the flow of information through neuronal networks. A key component of these organizational protein complexes is the family of synaptic adhesion proteins called neuroligins. Neuroligins form transsynaptic bridges with presynaptic neurexins to regulate various aspects of excitatory and inhibitory synaptic transmission. Neuroligin-2 (NLGN2) is the only member that acts exclusively at GABAergic inhibitory synapses. Altered expression and mutations in NLGN2 and several of its interacting partners are linked to cognitive and psychiatric disorders, including schizophrenia, autism, and anxiety. Research on NLGN2 has fundamentally shaped our understanding of the molecular architecture of inhibitory synapses. Here, we discuss the current knowledge on the molecular and cellular functions of mammalian NLGN2 and its role in the neuronal circuitry that regulates behavior in rodents and humans.

scholarly journals Rational thermostabilisation of four-helix bundle dimeric de novo proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shin Irumagawa ◽  
Kaito Kobayashi ◽  
Yutaka Saito ◽  
Takeshi Miyata ◽  
Mitsuo Umetsu ◽  
...  
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Protein Complexes ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Saturation Mutagenesis ◽  
Helix Bundle ◽  
Stable Mutant ◽  
Four Helix Bundle ◽  
The Stability

AbstractThe stability of proteins is an important factor for industrial and medical applications. Improving protein stability is one of the main subjects in protein engineering. In a previous study, we improved the stability of a four-helix bundle dimeric de novo protein (WA20) by five mutations. The stabilised mutant (H26L/G28S/N34L/V71L/E78L, SUWA) showed an extremely high denaturation midpoint temperature (Tm). Although SUWA is a remarkably hyperstable protein, in protein design and engineering, it is an attractive challenge to rationally explore more stable mutants. In this study, we predicted stabilising mutations of WA20 by in silico saturation mutagenesis and molecular dynamics simulation, and experimentally confirmed three stabilising mutations of WA20 (N22A, N22E, and H86K). The stability of a double mutant (N22A/H86K, rationally optimised WA20, ROWA) was greatly improved compared with WA20 (ΔTm = 10.6 °C). The model structures suggested that N22A enhances the stability of the α-helices and N22E and H86K contribute to salt-bridge formation for protein stabilisation. These mutations were also added to SUWA and improved its Tm. Remarkably, the most stable mutant of SUWA (N22E/H86K, rationally optimised SUWA, ROSA) showed the highest Tm (129.0 °C). These new thermostable mutants will be useful as a component of protein nanobuilding blocks to construct supramolecular protein complexes.

scholarly journals Stimulation of de novo glutathione synthesis by nitrofurantoin for enhanced resilience of hepatocytes

2021 ◽  
Author(s):  
Lukas S. Wijaya ◽  
Carina Rau ◽  
Theresa S. Braun ◽  
Serif Marangoz ◽  
Vincent Spegg ◽  
...  
Keyword(s):  
De Novo ◽  
Hepatoma Cell ◽  
Proteasome Inhibitors ◽  
Essential Element ◽  
Hepatoma Cell Line ◽  
Related Factor ◽  
Human Hepatoma Cell ◽  
Intact Cells ◽  
Intracellular Glutathione ◽  
Endogenous Antioxidant

AbstractToxicity is not only a function of damage mechanisms, but is also determined by cellular resilience factors. Glutathione has been reported as essential element to counteract negative influences. The present work hence pursued the question how intracellular glutathione can be elevated transiently to render cells more resistant toward harmful conditions. The antibiotic nitrofurantoin (NFT) was identified to stimulate de novo synthesis of glutathione in the human hepatoma cell line, HepG2, and in primary human hepatocytes. In intact cells, activation of NFT yielded a radical anion, which subsequently initiated nuclear-factor-erythroid 2-related-factor-2 (Nrf2)-dependent induction of glutamate cysteine ligase (GCL). Application of siRNA-based intervention approaches confirmed the involvement of the Nrf2-GCL axis in the observed elevation of intracellular glutathione levels. Quantitative activation of Nrf2 by NFT, and the subsequent rise in glutathione, were similar as observed with the potent experimental Nrf2 activator diethyl maleate. The elevation of glutathione levels, observed even 48 h after withdrawal of NFT, rendered cells resistant to different stressors such as the mitochondrial inhibitor rotenone, the redox cycler paraquat, the proteasome inhibitors MG-132 or bortezomib, or high concentrations of NFT. Repurpose of the antibiotic NFT as activator of Nrf2 could thus be a promising strategy for a transient and targeted activation of the endogenous antioxidant machinery.

scholarly journals Novel Dominant KCNQ2 Exon 7 Partial In-Frame Duplication in a Complex Epileptic and Neurodevelopmental Delay Syndrome

2020 ◽  
Vol 21 (12) ◽  
pp. 4447
Author(s):  
Pedro A. Lazo ◽  
Juan L. García ◽  
Paulino Gómez-Puertas ◽  
Íñigo Marcos-Alcalde ◽  
Cesar Arjona ◽  
...  
Keyword(s):  
Protein Function ◽  
De Novo ◽  
3D Structure ◽  
Unknown Origin ◽  
Unknown Etiology ◽  
Neurodevelopmental Delay ◽  
Calmodulin Binding ◽  
Whole Exome ◽  
Dynamics Simulations ◽  
Frame Duplication

Complex neurodevelopmental syndromes frequently have an unknown etiology, in which genetic factors play a pathogenic role. This study utilizes whole-exome sequencing (WES) to examine four members of a family with a son presenting, since birth, with epileptic-like crises, combined with cerebral palsy, severe neuromotor and developmental delay, dystonic tetraparexia, axonal motor affectation, and hyper-excitability of unknown origin. The WES study detected within the patient a de novo heterozygous in-frame duplication of thirty-six nucleotides within exon 7 of the human KCNQ2 gene. This insertion duplicates the first twelve amino acids of the calmodulin binding site I. Molecular dynamics simulations of this KCNQ2 peptide duplication, modelled on the 3D structure of the KCNQ2 protein, suggest that the duplication may lead to the dysregulation of calcium inhibition of this protein function.

scholarly journals 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography

2012 ◽  
Vol 180 (2) ◽  
pp. 318-326 ◽  
Author(s):  
Ke Wang ◽  
Korrinn Strunk ◽  
Gongpu Zhao ◽  
Jennifer L. Gray ◽  
Peijun Zhang
Keyword(s):  
Structure Determination ◽  
Mammalian Cells ◽  
Electron Tomography ◽  
3D Structure ◽  
Cryo Electron Tomography ◽  
3D Structure Determination

scholarly journals Atomic Electron Tomography: Probing 3D Structure and Material Properties at the Single-Atom Level

2017 ◽  
Vol 23 (S1) ◽  
pp. 1886-1887
Author(s):  
Yongsoo Yang ◽  
Chien-Chun Chen ◽  
M. C. Scott ◽  
Colin Ophus ◽  
Rui Xu ◽  
...  
Keyword(s):  
Material Properties ◽  
Electron Tomography ◽  
3D Structure ◽  
Atomic Electron ◽  
Single Atom ◽  
Atom Level

scholarly journals Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

2019 ◽  
Vol 476 (5) ◽  
pp. 809-826
Author(s):  
Karthik V. Rajasekar ◽  
Shuangxi Ji ◽  
Rachel J. Coulthard ◽  
Jon P. Ride ◽  
Gillian L. Reynolds ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Analytical Ultracentrifugation ◽  
De Novo ◽  
Learning Algorithm ◽  
Sequence Similarity ◽  
Homology Modelling ◽  
3D Structure ◽  
Large Family ◽  
Secreted Proteins ◽  
Self Incompatibility

Abstract SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a β-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15–18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.

Sign in / Sign up

Export Citation Format

Share Document