Your browser doesn't support javascript.
loading
: 20 | 50 | 100
1 - 20 de 68
1.
Commun Biol ; 7(1): 557, 2024 May 10.
Article En | MEDLINE | ID: mdl-38730276

The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.


Cryoelectron Microscopy , Capsid/metabolism , Capsid/ultrastructure , Capsid/chemistry , Cell Extracts , Saccharomyces cerevisiae/genetics , RNA, Viral/metabolism , RNA, Viral/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics
2.
Biomacromolecules ; 25(2): 778-791, 2024 Feb 12.
Article En | MEDLINE | ID: mdl-38190609

Considerable attention has been dedicated to lipid rafts due to their importance in numerous cell functions such as membrane trafficking, polarization, and signaling. Next to studies in living cells, artificial micrometer-sized vesicles with a minimal set of components are established as a major tool to understand the phase separation dynamics and their intimate interplay with membrane proteins. In parallel, mixtures of phospholipids and certain amphiphilic polymers simultaneously offer an interface for proteins and mimic this segregation behavior, presenting a tangible synthetic alternative for fundamental studies and bottom-up design of cellular mimics. However, the simultaneous insertion of complex and sensitive membrane proteins is experimentally challenging and thus far has been largely limited to natural lipids. Here, we present the co-reconstitution of the proton pump bo3 oxidase and the proton consumer ATP synthase in hybrid polymer/lipid giant unilamellar vesicles (GUVs) via fusion/electroformation. Variations of the current method allow for tailored reconstitution protocols and control of the vesicle size. In particular, mixing of protein-free and protein-functionalized nanosized vesicles in the electroformation film results in larger GUVs, while separate reconstitution of the respiratory enzymes enables higher ATP synthesis rates. Furthermore, protein labeling provides a synthetic mechanism for phase separation and protein sequestration, mimicking lipid- and protein-mediated domain formation in nature. The latter means opens further possibilities for re-enacting phenomena like supercomplex assembly or symmetry breaking and enriches the toolbox of bottom-up synthetic biology.


Polymers , Unilamellar Liposomes , Phospholipids , Membrane Proteins , Membrane Microdomains/metabolism , Adenosine Triphosphate
3.
Biochemistry ; 63(1): 82-93, 2024 Jan 02.
Article En | MEDLINE | ID: mdl-38085825

The pH dependence of the absorption and (time-resolved) fluorescence of two red-shifted fluorescent proteins, mCardinal and mNeptune, was investigated. Decay-associated spectra were measured following fluorescence excitation at 470 nm in PBS buffer with a pH that ranged from 5.5 to 8.0. The fluorescence of both proteins shows two different decay components. mCardinal exhibits an increase in the long-lived fluorescence component with acidification from 1.34 ns at pH 8.0 to 1.62 ns at pH 5.5. An additional fast decay component with 0.64 ns at pH 8.0 up to 1.1 ns at pH 5.5 was found to be blue-shifted compared to the long-lived component. The fluorescence lifetime of mNeptune is insensitive to pH. DAS of mCardinal were simulated assuming a coupled two-level system to describe the 1S state of the chromophore within two different conformations of the protein. MD simulations were conducted to correlate the experimentally observed pH-induced change in the lifetime in mCardinal with its molecular properties. While the chromophores of both protein variants are stabilized by the same number of hydrogen bonds, it was found that the chromophore in mCardinal exhibits more water contacts compared to mNeptune. In mCardinal, interaction between the chromophore and Glu-145 is reduced as compared to mNeptune, but interaction with Thr-147 which is Ser-147 in mNeptune is stronger in mCardinal. Therefore, the dynamics of the excited-state proton transfer (ESPT) might be different in mCardinal and mNeptune. The pH dependency of ESPT is suggested as a key mechanism for pH sensitivity.


Molecular Dynamics Simulation , Water , Hydrogen-Ion Concentration , Spectrometry, Fluorescence , Protons , Red Fluorescent Protein
4.
Nat Plants ; 9(8): 1359-1369, 2023 08.
Article En | MEDLINE | ID: mdl-37550369

The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure-functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution.


Photosystem II Protein Complex , alpha-Tocopherol , Photosystem II Protein Complex/metabolism , Cryoelectron Microscopy , alpha-Tocopherol/analysis , alpha-Tocopherol/metabolism , Thylakoids/metabolism , Photosynthesis , Plants/metabolism
5.
Protein Sci ; 32(9): e4753, 2023 09.
Article En | MEDLINE | ID: mdl-37572332

Within the cell, the trace element molybdenum (Mo) is only biologically active when complexed either within the nitrogenase-specific FeMo cofactor or within the molybdenum cofactor (Moco). Moco consists of an organic part, called molybdopterin (MPT) and an inorganic part, that is, the Mo-center. The enzyme which catalyzes the Mo-center formation is the molybdenum insertase (Mo-insertase). Mo-insertases consist of two functional domains called G- and E-domain. The G-domain catalyzes the formation of adenylated MPT (MPT-AMP), which is the substrate for the E-domain, that catalyzes the actual molybdate insertion reaction. Though the functions of E- and G-domain have been elucidated to great structural and mechanistic detail, their combined function is poorly characterized. In this work, we describe a structural model of the eukaryotic Mo-insertase Cnx1 complex that was generated based on cross-linking mass spectrometry combined with computational modeling. We revealed Cnx1 to form an asymmetric hexameric complex which allows the E- and G-domain active sites to align in a catalytic productive orientation toward each other.


Arabidopsis Proteins , Arabidopsis , Metalloproteins , Arabidopsis Proteins/chemistry , Calnexin/chemistry , Calnexin/metabolism , Arabidopsis/chemistry , Molybdenum/metabolism , Coenzymes/chemistry , Metalloproteins/chemistry , Pteridines/chemistry
6.
J Struct Biol X ; 8: 100094, 2023 Dec.
Article En | MEDLINE | ID: mdl-37638207

Biomolecular complexes and their interactions govern cellular structure and function. Understanding their architecture is a prerequisite for dissecting the cell's inner workings, but their higher-order assembly is often transient and challenging for structural analysis. Here, we performed cryo-EM on a single, highly heterogeneous biochemical fraction derived from Chaetomium thermophilum cell extracts to visualize the biomolecular content of the multicellular eukaryote. After cryo-EM single-particle image processing, results showed that a simultaneous three-dimensional structural characterization of multiple chemically diverse biomacromolecules is feasible. Namely, the thermophilic, eukaryotic complexes of (a) ATP citrate-lyase, (b) Hsp90, (c) 20S proteasome, (d) Hsp60 and (e) UDP-glucose pyrophosphorylase were characterized. In total, all five complexes have been structurally dissected in a thermophilic eukaryote in a total imaged sample area of 190.64 µm2, and two, in particular, 20S proteasome and Hsp60, exhibit side-chain resolution features. The C. thermophilum Hsp60 near-atomic model was resolved at 3.46 Å (FSC = 0.143) and shows a hinge-like conformational change of its equatorial domain, highly similar to the one previously shown for its bacterial orthologue, GroEL. This work demonstrates that cryo-EM of cell extracts will greatly accelerate the structural analysis of cellular complexes and provide unprecedented opportunities to annotate architectures of biomolecules in a holistic approach.

7.
Sci Rep ; 13(1): 8497, 2023 05 25.
Article En | MEDLINE | ID: mdl-37231156

The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53's C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53's C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).


Intrinsically Disordered Proteins , Tumor Suppressor Protein p53 , Humans , Tumor Suppressor Protein p53/metabolism , Computer Simulation , Intrinsically Disordered Proteins/chemistry , DNA/metabolism , Mass Spectrometry , Protein Binding
8.
Commun Biol ; 6(1): 552, 2023 05 22.
Article En | MEDLINE | ID: mdl-37217784

The oxoglutarate dehydrogenase complex (OGDHc) participates in the tricarboxylic acid cycle and, in a multi-step reaction, decarboxylates α-ketoglutarate, transfers succinyl to CoA, and reduces NAD+. Due to its pivotal role in metabolism, OGDHc enzymatic components have been studied in isolation; however, their interactions within the endogenous OGDHc remain elusive. Here, we discern the organization of a thermophilic, eukaryotic, native OGDHc in its active state. By combining biochemical, biophysical, and bioinformatic methods, we resolve its composition, 3D architecture, and molecular function at 3.35 Å resolution. We further report the high-resolution cryo-EM structure of the OGDHc core (E2o), which displays various structural adaptations. These include hydrogen bonding patterns confining interactions of OGDHc participating enzymes (E1o-E2o-E3), electrostatic tunneling that drives inter-subunit communication, and the presence of a flexible subunit (E3BPo), connecting E2o and E3. This multi-scale analysis of a succinyl-CoA-producing native cell extract provides a blueprint for structure-function studies of complex mixtures of medical and biotechnological value.


Citric Acid Cycle , Ketoglutarate Dehydrogenase Complex , Ketoglutarate Dehydrogenase Complex/chemistry , Ketoglutarate Dehydrogenase Complex/metabolism , Acyl Coenzyme A/metabolism , Cytoplasm
9.
J Exp Bot ; 74(12): 3630-3650, 2023 06 27.
Article En | MEDLINE | ID: mdl-37010230

EARLY FLOWERING 3 (ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation which will be essential for future plant breeding. To expand the limited knowledge on barley ELF3 in determining agronomic traits, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at the ELF3 locus, were compared for 10 developmental and yield-related traits. We determine novel exotic ELF3 alleles and show that HIF lines, carrying the exotic ELF3 allele, accelerated plant development compared with the cultivated ELF3 allele, depending on the genetic background. Remarkably, the most extreme effects on phenology could be attributed to one exotic ELF3 allele differing from the cultivated Barke ELF3 allele in only one single nucleotide polymorphism (SNP). This SNP causes an amino acid substitution (W669G), which as predicted has an impact on the protein structure of ELF3. Consequently, it may affect phase separation behaviour and nano-compartment formation of ELF3 and, potentially, also its local cellular interactions causing significant trait differences between HIF sister lines.


Hordeum , Quantitative Trait Loci , Chromosome Mapping , Hordeum/genetics , Alleles , Plant Breeding , Plant Development
10.
J Biol Chem ; 299(6): 104756, 2023 06.
Article En | MEDLINE | ID: mdl-37116705

Phosphatidylserine (PS) synthase from Candida albicans, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis. Rational drug design or small molecule screening are effective ways to identify specific inhibitors of Cho1, but both will be facilitated by protein purification. Due to the transmembrane nature of Cho1, methods were needed to solubilize and purify the native form of Cho1. Here, we used six non-ionic detergents and three styrene maleic acids (SMAs) to solubilize an HA-tagged Cho1 protein from the total microsomal fractions. Blue native PAGE and immunoblot analysis revealed a single band corresponding to Cho1 in all detergent-solubilized fractions, while two bands were present in the SMA2000-solubilized fraction. Our enzymatic assay suggests that digitonin- or DDM-solubilized enzyme has the most PS synthase activity. Pull-downs of HA-tagged Cho1 from the digitonin-solubilized fraction reveal an apparent MW of Cho1 consistent with a hexamer. Furthermore, negative-staining electron microscopy analysis and AlphaFold2 structure prediction modeling suggest the hexamer is composed of a trimer of dimers. We purified Cho1 protein to near-homogeneity as a hexamer using affinity chromatography and TEV protease treatment, and optimized Cho1 enzyme activity for manganese and detergent concentrations, temperature (24 °C), and pH (8.0). The purified Cho1 has a Km for its substrate CDP-diacylglycerol of 72.20 µM with a Vmax of 0.079 nmol/(µg∗min) while exhibiting a sigmoidal kinetic curve for its other substrate serine, indicating cooperative binding. Purified hexameric Cho1 can potentially be used in downstream structure determination and small drug screening.


CDPdiacylglycerol-Serine O-Phosphatidyltransferase , Candida albicans , Candida albicans/enzymology , CDPdiacylglycerol-Serine O-Phosphatidyltransferase/chemistry , Detergents/pharmacology , Digitonin/metabolism
11.
Proteomics ; 23(17): e2200096, 2023 09.
Article En | MEDLINE | ID: mdl-37016452

In the cellular context, proteins participate in communities to perform their function. The detection and identification of these communities as well as in-community interactions has long been the subject of investigation, mainly through proteomics analysis with mass spectrometry. With the advent of cryogenic electron microscopy and the "resolution revolution," their visualization has recently been made possible, even in complex, native samples. The advances in both fields have resulted in the generation of large amounts of data, whose analysis requires advanced computation, often employing machine learning approaches to reach the desired outcome. In this work, we first performed a robust proteomics analysis of mass spectrometry (MS) data derived from a yeast native cell extract and used this information to identify protein communities and inter-protein interactions. Cryo-EM analysis of the cell extract provided a reconstruction of a biomolecule at medium resolution (∼8 Å (FSC = 0.143)). Utilizing MS-derived proteomics data and systematic fitting of AlphaFold-predicted atomic models, this density was assigned to the 2.6 MDa complex of yeast fatty acid synthase. Our proposed workflow identifies protein complexes in native cell extracts from Saccharomyces cerevisiae by combining proteomics, cryo-EM, and AI-guided protein structure prediction.


Proteomics , Saccharomyces cerevisiae , Cell Extracts , Cryoelectron Microscopy/methods , Proteins/chemistry
12.
Mol Syst Biol ; 19(4): e11587, 2023 04 12.
Article En | MEDLINE | ID: mdl-36896624

Integration of experimental and computational methods is crucial to better understanding protein-protein interactions (PPIs), ideally in their cellular context. In their recent work, Rappsilber and colleagues (O'Reilly et al, 2023) identified bacterial PPIs using an array of approaches. They combined whole-cell crosslinking, co-fractionation mass spectrometry, and open-source data mining with artificial intelligence (AI)-based structure prediction of PPIs in the well-studied organism Bacillus subtilis. This innovative approach reveals architectural knowledge for in-cell PPIs that are often lost upon cell lysis, making it applicable to genetically intractable organisms such as pathogenic bacteria.


Artificial Intelligence , Protein Interaction Mapping , Protein Interaction Mapping/methods , Proteins
13.
J Colloid Interface Sci ; 634: 300-313, 2023 Mar 15.
Article En | MEDLINE | ID: mdl-36535166

HYPOTHESIS: Lipophilic cannabidiol can be solubilized in oil-in water nanoemulsions, which can then be impregnated into chitosan hydrogels forming another colloidal system that will facilitate cannabidiol's release. The delivery from both systems was compared, alongside structural and biological studies, to clarify the effect of the two carriers' structure on the release and toxicity of the systems. EXPERIMENTS: Oil-in-water nanoemulsions (NEs) and the respective nanoemulsion-filled chitosan hydrogels (NE/HGs) were formulated as carriers of cannabidiol (CBD). Size, polydispersity and stability of the NEs were evaluated and then membrane dynamics, shape and structure of both systems were investigated with EPR spin probing, SAXS and microscopy. Biocompatibility of the colloidal delivery systems was evaluated through cytotoxicity tests over normal human skin fibroblasts. An ex vivo permeation protocol using porcine ear skin was implemented to assess the release of CBD and its penetration through the skin. FINDINGS: Incorporation of the NEs in chitosan hydrogels does not significantly affect their structural properties as evidenced through SAXS, EPR and confocal microscopy. These findings indicate the successful development of a novel nanocarrier that preserves the NE structure with the CBD remaining encapsulated in the oil core while providing new rheological properties advantageous over NEs. Moreover, NE/HGs proved to be more efficient as a carrier for the release of CBD. Cell viability assessment revealed high biocompatibility of the proposed colloids.


Cannabidiol , Chitosan , Humans , Animals , Swine , Hydrogels/chemistry , Scattering, Small Angle , Emulsions/chemistry , X-Ray Diffraction , Water/chemistry
14.
Protein Sci ; 32(1): e4523, 2023 01.
Article En | MEDLINE | ID: mdl-36454539

Understanding protein-protein interactions (PPIs) is fundamental to infer how different molecular systems work. A major component to model molecular recognition is the buried surface area (BSA), that is, the area that becomes inaccessible to solvent upon complex formation. To date, many attempts tried to connect BSA to molecular recognition principles, and in particular, to the underlying binding affinity. However, the most popular approach to calculate BSA is to use a single (or in some cases few) bound structures, consequently neglecting a wealth of structural information of the interacting proteins derived from ensembles corresponding to their unbound and bound states. Moreover, the most popular method inherently assumes the component proteins to bind as rigid entities. To address the above shortcomings, we developed a Monte Carlo method-based Interface Residue Assessment Algorithm (IRAA), to calculate a combined distribution of BSA for a given complex. Further, we apply our algorithm to human ACE2 and SARS-CoV-2 Spike protein complex, a system of prime importance. Results show a much broader distribution of BSA compared to that obtained from only the bound structure or structures and extended residue members of the interface with implications to the underlying biomolecular recognition. We derive that specific interface residues of ACE2 and of S-protein are consistently highly flexible, whereas other residues systematically show minor conformational variations. In effect, IRAA facilitates the use of all available structural data for any biomolecular complex of interest, extracting quantitative parameters with statistical significance, thereby providing a deeper biophysical understanding of the molecular system under investigation.


COVID-19 , Humans , Angiotensin-Converting Enzyme 2/metabolism , Binding Sites , Protein Binding , Proteins/metabolism , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Algorithms
15.
Biomacromolecules ; 23(12): 5084-5094, 2022 Dec 12.
Article En | MEDLINE | ID: mdl-36399657

New technologies for purifying membrane-bound protein complexes in combination with cryo-electron microscopy (EM) have recently allowed the exploration of such complexes under near-native conditions. In particular, polymer-encapsulated nanodiscs enable the study of membrane proteins at high resolution while retaining protein-protein and protein-lipid interactions within a lipid bilayer. However, this powerful technology has not been exploited to address the important question of how endogenous─as opposed to overexpressed─membrane proteins are organized within a lipid environment. In this work, we demonstrate that biochemical enrichment protocols for native membrane-protein complexes from Chaetomium thermophilum in combination with polymer-based lipid-bilayer nanodiscs provide a substantial improvement in the quality of recovered endogenous membrane-protein complexes. Mass spectrometry results revealed ∼1123 proteins, while multiple 2D class averages and two 3D reconstructions from cryo-EM data furnished prominent structural signatures. This integrated methodological approach to enriching endogenous membrane-protein complexes provides unprecedented opportunities for a deeper understanding of eukaryotic membrane proteomes.


Lipid Bilayers , Nanostructures , Lipid Bilayers/chemistry , Cryoelectron Microscopy/methods , Membrane Proteins/chemistry , Eukaryota/metabolism , Nanostructures/chemistry , Polymers/chemistry
16.
Nature ; 611(7935): 399-404, 2022 Nov.
Article En | MEDLINE | ID: mdl-36289347

The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast1. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT2. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid3 and glucose4 signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators.


Cryoelectron Microscopy , GTPase-Activating Proteins , Multienzyme Complexes , Animals , GTP Phosphohydrolases/chemistry , GTP Phosphohydrolases/metabolism , GTP Phosphohydrolases/ultrastructure , GTPase-Activating Proteins/chemistry , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/ultrastructure , Mammals , Mechanistic Target of Rapamycin Complex 1/metabolism , Multienzyme Complexes/chemistry , Multienzyme Complexes/metabolism , Multienzyme Complexes/ultrastructure , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/ultrastructure , Protein Subunits/chemistry , Protein Subunits/metabolism , Amino Acids , Glucose , COP-Coated Vesicles/chemistry , COP-Coated Vesicles/metabolism
17.
Langmuir ; 38(28): 8595-8606, 2022 07 19.
Article En | MEDLINE | ID: mdl-35786894

Investigating how hydrophobic molecules mix with phospholipid bilayers and how they affect membrane properties is commonplace in biophysics. Despite this, a molecular-level empirical description of a membrane model as simple as a phospholipid bilayer with long linear hydrophobic chains incorporated is still missing. Here, we present an unprecedented molecular characterization of the incorporation of two long n-alkanes, n-eicosane (C20) and n-triacontane (C30) with 20 and 30 carbons, respectively, in phosphatidylcholine (PC) bilayers using a combination of experimental techniques (2H NMR, 31P NMR, 1H-13C dipolar recoupling solid-state NMR, X-ray scattering, and cryogenic electron microscopy) and atomistic molecular dynamics (MD) simulations. At low hydration, deuterated C20 and C30 yield 2H NMR spectra evidencing anisotropic-motion, which demonstrates their miscibility in PC membranes up to a critical alkane-to-acyl-chain volume fraction, ϕc. The acquired 2H NMR spectra of C20 and C30 have notably different lineshapes. At low alkane volume fractions below ϕc, CHARMM36 MD simulations predict such 2H NMR spectra qualitatively and thus enable an atomistic-level interpretation of the spectra. Above ϕc, the 2H NMR lineshapes become characteristic of motions in the intermediate-regime that, together with the MD simulation results, suggest the onset of immiscibility between the alkane molecules and the acyl chains. For all the systems investigated, the phospholipid molecular structure is unperturbed by the presence of the alkanes. However, at conditions of excess hydration and at surprisingly low alkane fractions below ϕc, a peak characteristic of isotropic motion is observed in both the 2H spectra of the alkanes and 31P spectra of the phospholipids, strongly indicating that the incorporation of the alkanes induces a reduction on the average radius of the lipid vesicles.


Lipid Bilayers , Phospholipids , Alkanes , Lipid Bilayers/chemistry , Magnetic Resonance Spectroscopy , Phosphatidylcholines/chemistry , Phospholipids/chemistry
18.
Proc Natl Acad Sci U S A ; 119(20): e2122468119, 2022 05 17.
Article En | MEDLINE | ID: mdl-35549547

Due to their augmented properties, biomimetic polymer/lipid hybrid compartments are a promising substitute for natural liposomes in multiple applications, but the protein-free fusion of those semisynthetic membranes is unexplored to date. Here, we study the charge-mediated fusion of hybrid vesicles composed of poly(dimethylsiloxane)-graft-poly(ethylene oxide) and different lipids and analyze the process by size distribution and the mixing of membrane species at µm and nano scales. Remarkably, the membrane mixing of oppositely charged hybrids surpasses by far the degree in liposomes, which we correlate with properties like membrane disorder, rigidity, and ability of amphiphiles for flip-flop. Furthermore, we employ the integration of two respiratory proteins as a functional content mixing assay for different membrane compositions. This reveals that fusion is also attainable with neutral and cationic hybrids and that the charge is not the sole determinant of the final adenosine triphosphate synthesis rate, substantiating the importance of reconstitution environment. Finally, we employ this fusion strategy for the delivery of membrane proteins to giant unilamellar vesicles as a way to automate the assembly of synthetic cells.


Dimethylpolysiloxanes , Drug Delivery Systems , Polyethylene Glycols , Dimethylpolysiloxanes/chemistry , Membranes, Artificial , Phospholipids/chemistry , Polyethylene Glycols/chemistry
19.
J Mol Biol ; 434(13): 167637, 2022 07 15.
Article En | MEDLINE | ID: mdl-35595165

After two years since the outbreak, the COVID-19 pandemic remains a global public health emergency. SARS-CoV-2 variants with substitutions on the spike (S) protein emerge increasing the risk of immune evasion and cross-species transmission. Here, we analyzed the evolution of the S protein as recorded in 276,712 samples collected before the start of vaccination efforts. Our analysis shows that most variants destabilize the S protein trimer, increase its conformational heterogeneity and improve the odds of the recognition by the host cell receptor. Most frequent substitutions promote overall hydrophobicity by replacing charged amino acids, reducing stabilizing local interactions in the unbound S protein trimer. Moreover, our results identify "forbidden" regions that rarely show any sequence variation, and which are related to conformational changes occurring upon fusion. These results are significant for understanding the structure and function of SARS-CoV-2 related proteins which is a critical step in vaccine development and epidemiological surveillance.


COVID-19 , Spike Glycoprotein, Coronavirus , Angiotensin-Converting Enzyme 2 , COVID-19/epidemiology , Humans , Pandemics/prevention & control , Protein Binding , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
20.
Plant Commun ; 3(1): 100248, 2022 01 10.
Article En | MEDLINE | ID: mdl-35059628

Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.


Cyanobacteria , Photosystem I Protein Complex , Chlorophyll , Cryoelectron Microscopy , Cyanobacteria/chemistry , Cyanobacteria/metabolism , Photosynthesis , Photosystem I Protein Complex/chemistry , Photosystem I Protein Complex/metabolism
...