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1.
EMBO J ; 41(4): e106523, 2022 02 15.
Article in English | MEDLINE | ID: mdl-34935159

ABSTRACT

Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in structural and molecular diversity of dendritic spines. Active spines with large calcium ion (Ca2+ ) transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into spines via the actin-based motor myosin V. An increase in synaptic strength correlates with stable anchoring of the ER, followed by the formation of an organelle referred to as the spine apparatus. Here, we show that myosin V binds the Ca2+ sensor caldendrin, a brain-specific homolog of the well-known myosin V interactor calmodulin. While calmodulin is an essential activator of myosin V motor function, we found that caldendrin acts as an inhibitor of processive myosin V movement. In mouse and rat hippocampal neurons, caldendrin regulates spine apparatus localization to a subset of dendritic spines through a myosin V-dependent pathway. We propose that caldendrin transforms myosin into a stationary F-actin tether that enables the localization of ER tubules and formation of the spine apparatus in dendritic spines.


Subject(s)
Calcium-Binding Proteins/metabolism , Dendritic Spines/metabolism , Endoplasmic Reticulum/metabolism , Myosin Type V/metabolism , Actins/metabolism , Animals , Calcium-Binding Proteins/genetics , Calmodulin/metabolism , Endoplasmic Reticulum, Smooth/metabolism , HEK293 Cells , Hippocampus/cytology , Hippocampus/metabolism , Humans , Mass Spectrometry , Mice, Knockout , Myosin Type V/genetics , Protein Interaction Domains and Motifs , Rats, Wistar
2.
J Virol ; 98(3): e0157623, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38323814

ABSTRACT

Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development. IMPORTANCE: Our study delves into the structural aspects of adenovirus (AdV) infections, specifically HAdV-C5 in the respiratory epithelium. It uncovers the molecular details of a novel pathway where human lactoferrin (hLF) interacts with the major capsid protein, hexon, facilitating viral entry, and bypassing traditional receptors such as CAR and integrins. The study's cryo-EM structures reveal how hLF engages hexon, primarily through its N-terminal lactoferricin (Lfcin) region and hexon's hypervariable region 1 (HVR-1). Mutational analyses identify critical Lfcin contacts and other regions within hLF vital for hexon binding. This structural insight sheds light on HAdV-C5's mechanism of utilizing soluble hLF/Lfcin for cellular entry, holding promise for gene therapy and vaccine development advancements in adenovirus research.


Subject(s)
Adenoviruses, Human , Capsid Proteins , Lactoferrin , Receptors, Virus , Virus Internalization , Humans , Adenovirus Infections, Human/metabolism , Adenovirus Infections, Human/virology , Adenoviruses, Human/chemistry , Adenoviruses, Human/genetics , Adenoviruses, Human/metabolism , Adenoviruses, Human/ultrastructure , Binding Sites/genetics , Capsid Proteins/chemistry , Capsid Proteins/genetics , Capsid Proteins/metabolism , Capsid Proteins/ultrastructure , Cryoelectron Microscopy , Lactoferrin/chemistry , Lactoferrin/genetics , Lactoferrin/metabolism , Lactoferrin/ultrastructure , Models, Biological , Mutation , Protein Binding , Receptors, Virus/chemistry , Receptors, Virus/genetics , Receptors, Virus/metabolism , Receptors, Virus/ultrastructure , Solubility , Respiratory Mucosa/cytology , Respiratory Mucosa/metabolism , Respiratory Mucosa/virology
3.
Chemistry ; 30(49): e202402151, 2024 Sep 02.
Article in English | MEDLINE | ID: mdl-38924659

ABSTRACT

Reactive N-hydroxy-9-azabicyclo[3.3.1]nonane (ABNOH) linked 2'-deoxyuridine 5'-O-mono- and triphosphates were synthesized through a CuAAC reaction of ABNOH-PEG4-N3 with 5-ethynyl-dUMP or -dUTP. The modified triphosphate was used as substrate for enzymatic synthesis of modified DNA probes with KOD XL DNA polymerase. The keto-ABNO radical reacted with tryptophan (Trp) and Trp-containing peptides to form a stable tricyclic fused hexahydropyrrolo-indole conjugates. Similarly modified ABNOH-linked nucleotides reacted with Trp-containing peptides to form a stable conjugate in the presence but surprisingly even in the absence of NaNO2 (presumably through activation by O2). The reactive ABNOH-modified DNA probe was used for bioconjugations and crosslinking with Trp-containing peptides or proteins.


Subject(s)
DNA , Nucleotides , Peptides , Tryptophan , Tryptophan/chemistry , DNA/chemistry , Peptides/chemistry , Nucleotides/chemistry , Proteins/chemistry , Cross-Linking Reagents/chemistry , DNA-Directed DNA Polymerase/metabolism , DNA-Directed DNA Polymerase/chemistry
4.
Anal Chem ; 95(44): 16123-16130, 2023 11 07.
Article in English | MEDLINE | ID: mdl-37877738

ABSTRACT

Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.


Subject(s)
Proteomics , Tandem Mass Spectrometry , Proteomics/methods , Tandem Mass Spectrometry/methods , Ubiquitin , Cyclotrons , Fourier Analysis
5.
Anal Bioanal Chem ; 415(18): 4209-4220, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37014373

ABSTRACT

MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm-1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.


Subject(s)
Capsid , Electrons , Computer Simulation , Synchrotrons , X-Rays
6.
Drug Discov Today Technol ; 39: 89-99, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34906329

ABSTRACT

During the last years, X-ray free electron lasers (XFELs) have emerged as X-ray sources of unparalleled brightness, delivering extreme amounts of photons in femtosecond pulses. As such, they have opened up completely new possibilities in drug discovery and structural biology, including studying high resolution biomolecular structures and their functioning in a time resolved manner, and diffractive imaging of single particles without the need for their crystallization. In this perspective, we briefly review the operation of XFELs, their immediate uses for drug discovery and focus on the potentially revolutionary single particle diffractive imaging technique and the challenges which remain to be overcome to fully realize its potential to provide high resolution structures without the need for crystallization, freezing or the need to keep proteins stable at extreme concentrations for long periods of time. As the issues have been to a large extent sample delivery related, we outline a way for native mass spectrometry to overcome these and enable so far impossible research with a potentially huge impact on structural biology and drug discovery, such as studying structures of transient intermediate species in viral life cycles or during functioning of molecular machines.


Subject(s)
Electrons , Lasers , Mass Spectrometry , X-Ray Diffraction , X-Rays
7.
Mol Cell Proteomics ; 18(2): 320-337, 2019 02.
Article in English | MEDLINE | ID: mdl-30459217

ABSTRACT

Eukaryotic protein homeostasis (proteostasis) is largely dependent on the action of highly conserved Hsp70 molecular chaperones. Recent evidence indicates that, apart from conserved molecular allostery, Hsp70 proteins have retained and adapted the ability to assemble as functionally relevant ATP-bound dimers throughout evolution. Here, we have compared the ATP-dependent dimerization of DnaK, human stress-inducible Hsp70, Hsc70 and BiP Hsp70 proteins, showing that their dimerization propensities differ, with stress-inducible Hsp70 being predominantly dimeric in the presence of ATP. Structural analyses using hydrogen/deuterium exchange mass spectrometry, native electrospray ionization mass spectrometry and small-angle X-ray scattering revealed that stress-inducible Hsp70 assembles in solution as an antiparallel dimer with the intermolecular interface closely resembling the ATP-bound dimer interfaces captured in DnaK and BiP crystal structures. ATP-dependent dimerization of stress-inducible Hsp70 is necessary for its efficient interaction with Hsp40, as shown by experiments with dimerization-deficient mutants. Moreover, dimerization of ATP-bound Hsp70 is required for its participation in high molecular weight protein complexes detected ex vivo, supporting its functional role in vivo As human cytosolic Hsp70 can interact with tetratricopeptide repeat (TPR) domain containing cochaperones, we tested the interaction of Hsp70 ATP-dependent dimers with Chip and Tomm34 cochaperones. Although Chip associates with intact Hsp70 dimers to form a larger complex, binding of Tomm34 disrupts the Hsp70 dimer and this event plays an important role in Hsp70 activity regulation. In summary, this study provides structural evidence of robust ATP-dependent antiparallel dimerization of human inducible Hsp70 protein and suggests a novel role of TPR domain cochaperones in multichaperone complexes involving Hsp70 ATP-bound dimers.


Subject(s)
Adenosine Triphosphate/metabolism , HSP70 Heat-Shock Proteins/chemistry , HSP70 Heat-Shock Proteins/metabolism , Mitochondrial Membrane Transport Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Crystallography, X-Ray , HEK293 Cells , Humans , Mitochondrial Precursor Protein Import Complex Proteins , Models, Molecular , Protein Binding , Protein Multimerization , Scattering, Small Angle , Stress, Physiological
8.
Anal Chem ; 91(17): 10970-10978, 2019 09 03.
Article in English | MEDLINE | ID: mdl-31408320

ABSTRACT

Insight into the structure-function relationship of membrane proteins is important to understand basic cell function and inform drug development, as these are common targets for drugs. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established technique for the study of protein conformational dynamics and has shown compatibility with membrane proteins. However, the digestion and mass analysis of peptides from membrane proteins can be challenging, severely limiting the HDX-MS experiment. Here we compare the digestion of four integral membrane proteins-Cl-/H+ exchange transporter (ClC-ec1), leucine transporter (LeuT), dopamine transporter (DAT), and serotonin transporter (SERT)-by the use of porcine pepsin and three alternative aspartic proteases either in-solution or immobilized on-column in an optimized HDX-MS-compatible workflow. Pepsin was the most favorable for the digestion of ClC-ec1 and LeuT, providing coverage of 82.2 and 33.2% of the respective protein sequence; however, the alternative proteases surpassed pepsin for the digestion of DAT and SERT. By also screening quench solution additives, we observe that the denaturant urea was beneficial, resulting in improved sequence coverage of all membrane proteins, in contrast to guanidine hydrochloride. Furthermore, significant improvements in sequence coverage were achieved by tailoring the chromatography to handle hydrophobic peptides. Overall, we demonstrate that the susceptibility of membrane proteins to proteolytic digestion during HDX-MS is highly protein-specific. Our results highlight the importance of having multiple proteases and different quench buffer additives in the HDX-MS toolbox and the need to carefully screen a range of digestion conditions to successfully optimize the HDX-MS analysis of integral membrane proteins.


Subject(s)
Antiporters/analysis , Dopamine Plasma Membrane Transport Proteins/analysis , Drosophila Proteins/analysis , Escherichia coli Proteins/analysis , Hydrogen Deuterium Exchange-Mass Spectrometry/methods , Peptide Fragments/analysis , Serotonin Plasma Membrane Transport Proteins/analysis , Amino Acid Sequence , Animals , Antiporters/chemistry , Aquifex , Aspartic Acid Proteases/chemistry , Bacteria , Dopamine Plasma Membrane Transport Proteins/chemistry , Drosophila Proteins/chemistry , Drosophila melanogaster , Escherichia coli , Escherichia coli Proteins/chemistry , Humans , Models, Molecular , Pepsin A/chemistry , Proteolysis , Serotonin Plasma Membrane Transport Proteins/chemistry , Structure-Activity Relationship , Swine , Urea/chemistry
9.
Biochim Biophys Acta Gen Subj ; 1861(2): 157-167, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27851982

ABSTRACT

BACKGROUND: Cellobiose dehydrogenase (CDH) is a fungal extracellular oxidoreductase which fuels lytic polysaccharide monooxygenase with electrons during cellulose degradation. Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. METHODS: To investigate the structural aspects underlying the domain interaction in CDH, hydrogen/deuterium exchange (HDX-MS) with improved proteolytic setup (combination of nepenthesin-1 with rhizopuspepsin), native mass spectrometry with ion mobility and electrostatics calculations were used. RESULTS: HDX-MS revealed pH-dependent changes in solvent accessibility and hydrogen bonding at the interdomain interface. Electrostatics calculations identified these differences to result from charge neutralization by protonation and together with ion mobility pointed at higher electrostatic repulsion between CDH domains at neutral pH. In addition, we uncovered extensive O-glycosylation in the linker region and identified the long-unknown exact cleavage point in papain-mediated domain separation. CONCLUSIONS: Transition of CDH between its inactive (open) and interdomain electron transfer-capable (closed) state is shown to be governed by changes in the protein surface electrostatics at the domain interface. Our study confirms that the interdomain electrostatic repulsion is the key factor modulating the functioning of CDH. GENERAL SIGNIFICANCE: The results presented in this paper provide experimental evidence for the role of charge repulsion in the interdomain electron transfer in cellobiose dehydrogenases, which is relevant for exploiting their biotechnological potential in biosensors and biofuel cells.


Subject(s)
Carbohydrate Dehydrogenases/metabolism , Cellobiose/metabolism , Electron Transport/physiology , Amino Acid Sequence , Cytochromes/metabolism , Deuterium/metabolism , Electrons , Flavins/metabolism , Fungal Proteins/metabolism , Fungi/metabolism , Glycosylation , Hydrogen/metabolism , Hydrogen-Ion Concentration , Mixed Function Oxygenases/metabolism , Polysaccharides/metabolism , Protein Domains , Proteolysis , Static Electricity
10.
J Biol Chem ; 290(26): 16246-60, 2015 Jun 26.
Article in English | MEDLINE | ID: mdl-25971962

ABSTRACT

Phosducin (Pdc), a highly conserved phosphoprotein involved in the regulation of retinal phototransduction cascade, transcriptional control, and modulation of blood pressure, is controlled in a phosphorylation-dependent manner, including the binding to the 14-3-3 protein. However, the molecular mechanism of this regulation is largely unknown. Here, the solution structure of Pdc and its interaction with the 14-3-3 protein were investigated using small angle x-ray scattering, time-resolved fluorescence spectroscopy, and hydrogen-deuterium exchange coupled to mass spectrometry. The 14-3-3 protein dimer interacts with Pdc using surfaces both inside and outside its central channel. The N-terminal domain of Pdc, where both phosphorylation sites and the 14-3-3-binding motifs are located, is an intrinsically disordered protein that reduces its flexibility in several regions without undergoing dramatic disorder-to-order transition upon binding to 14-3-3. Our data also indicate that the C-terminal domain of Pdc interacts with the outside surface of the 14-3-3 dimer through the region involved in Gtßγ binding. In conclusion, we show that the 14-3-3 protein interacts with and sterically occludes both the N- and C-terminal Gtßγ binding interfaces of phosphorylated Pdc, thus providing a mechanistic explanation for the 14-3-3-dependent inhibition of Pdc function.


Subject(s)
14-3-3 Proteins/chemistry , 14-3-3 Proteins/metabolism , Eye Proteins/chemistry , Eye Proteins/metabolism , GTP-Binding Protein Regulators/chemistry , GTP-Binding Protein Regulators/metabolism , Phosphoproteins/chemistry , Phosphoproteins/metabolism , 14-3-3 Proteins/genetics , Amino Acid Sequence , Animals , Binding Sites , Eye Proteins/genetics , GTP-Binding Protein Regulators/genetics , Humans , Models, Molecular , Phosphoproteins/genetics , Phosphorylation , Protein Binding , Protein Structure, Tertiary , Rats
11.
Anal Chem ; 87(13): 6681-7, 2015 Jul 07.
Article in English | MEDLINE | ID: mdl-25993527

ABSTRACT

The pitcher secretions of the Nepenthes genus of carnivorous plants contain a proteolytic activity that is very useful for hydrogen/deuterium exchange mass spectrometry (HX-MS). Our efforts to reconstitute pitcher fluid activity using recombinant nepenthesin I (one of two known aspartic proteases in the fluid) revealed a partial cleavage profile and reduced enzymatic stability in certain HX-MS applications. We produced and characterized recombinant nepenthesin II to determine if it complemented nepenthesin I in HX-MS applications. Nepenthesin II shares many properties with nepenthesin I, such as fast digestion at reduced temperature and pH, and broad cleavage specificity, but in addition, it cleaves C-terminal to tryptophan. Neither enzyme reproduces the C-terminal proline cleavage we observed in the natural extract. Nepenthesin II is considerably more resistant to chemical denaturants and reducing agents than nepenthesin I, and it possesses a stability profile that is similar to that of pepsin. Higher stability combined with the slightly broader cleavage specificity makes nepenthesin II a useful alternative to pepsin and a more complete replacement for pitcher fluid in HX-MS applications.


Subject(s)
Mass Spectrometry/methods , Deuterium/chemistry , Deuterium Exchange Measurement/methods , Recombinant Proteins/chemistry
12.
Anal Chem ; 86(9): 4287-94, 2014 May 06.
Article in English | MEDLINE | ID: mdl-24661217

ABSTRACT

Hydrogen/deuterium exchange coupled to mass spectrometry (HXMS) utilizes enzymatic digestion of proteins to localize the information about altered exchange patterns in protein structure. The ability of the protease to produce small peptides and overlapping fragments and provide sufficient coverage of the protein sequence is essential for localizing regions of interest. Recently, it was shown that there is an interesting group of proteolytic enzymes from carnivorous pitcher plants of the genus Nepenthes. In this report, we describe successful immobilization and the use of one of these enzymes, nepenthesin-1, in HXMS workflow. In contrast to pepsin, it has different cleavage specificities, and despite its high inherent susceptibility to reducing and denaturing agents, it is very stable upon immobilization and withstands even high concentration of guanidine hydrochloride and reducing agents. We show that denaturing agents can alter digestion by reducing protease activity and/or substrate solubility, and additionally, they influence the trapping of proteolytic peptides onto the reversed phase resin.


Subject(s)
Aspartic Acid Proteases/metabolism , Tandem Mass Spectrometry/methods , Chromatography, Liquid , Deuterium , Hydrogen
13.
Protein Expr Purif ; 95: 121-8, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24365662

ABSTRACT

Carnivorous plants of the genus Nepenthes produce their own aspartic proteases, nepenthesins, to digest prey trapped in their pitchers. Nepenthesins differ significantly in sequence from other aspartic proteases in the animal or even plant kingdoms. This difference, which also brings more cysteine residues into the structure of these proteases, can be a cause of uniquely high temperature and pH stabilities of nepenthesins. Their detailed structure characterization, however, has not previously been possible due to low amounts of protease present in the pitcher fluid and also due to limited accessibility of Nepenthes plants. In the present study we describe a convenient way for obtaining high amounts of nepenthesin-1 from Nepenthes gracilis using heterologous production in Escherichia coli. The protein can be easily refolded in vitro and its characteristics are very close to those described for a natural enzyme isolated from the pitcher fluid. Similarly to the natural enzyme, recombinant nepenthesin-1 is sensitive to denaturing and reducing agents. It also has maximal activity around pH 2.5, shows unusual stability at high pH and its activity is not irreversibly inhibited even after prolonged incubation in the basic pH range. On the other hand, temperature stability of the recombinant enzyme is lower in comparison with the natural enzyme, which can be attributed to missing N-glycosylation in the recombinant protein.


Subject(s)
Aspartic Acid Proteases/chemistry , Magnoliopsida/enzymology , Plant Proteins/chemistry , Recombinant Proteins/chemistry , Aspartic Acid Proteases/genetics , Aspartic Acid Proteases/metabolism , Carnivory , Disulfides , Enzyme Stability , Hydrogen-Ion Concentration , Magnoliopsida/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Reducing Agents , Temperature
14.
FEBS Lett ; 598(4): 485-499, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38243391

ABSTRACT

Primary hyperoxaluria type I (PH1) is caused by deficient alanine:glyoxylate aminotransferase (AGT) activity. PH1-causing mutations in AGT lead to protein mistargeting and aggregation. Here, we use hydrogen-deuterium exchange (HDX) to characterize the wild-type (WT), the LM (a polymorphism frequent in PH1 patients) and the LM G170R (the most common mutation in PH1) variants of AGT. We provide the first experimental analysis of AGT structural dynamics, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants only show local destabilization. Enzymatic transamination of the pyridoxal 5-phosphate cofactor bound to AGT hardly affects stability. Our study, thus, supports that AGT misfolding is not caused by dramatic effects on structural dynamics.


Subject(s)
Hyperoxaluria, Primary , Transaminases , Humans , Hyperoxaluria, Primary/genetics , Hyperoxaluria, Primary/metabolism , Mutation , Polymorphism, Genetic , Transaminases/chemistry
15.
Methods Mol Biol ; 2648: 99-122, 2023.
Article in English | MEDLINE | ID: mdl-37039988

ABSTRACT

Hydrogen/deuterium exchange (HDX) is a well-established analytical technique that enables monitoring of protein dynamics and interactions by probing the isotope exchange of backbone amides. It has virtually no limitations in terms of protein size, flexibility, or reaction conditions and can thus be performed in solution at different pH values and temperatures under controlled redox conditions. Thanks to its coupling with mass spectrometry (MS), it is also straightforward to perform and has relatively high throughput, making it an excellent complement to the high-resolution methods of structural biology. Given the recent expansion of artificial intelligence-aided protein structure modeling, there is considerable demand for techniques allowing fast and unambiguous validation of in silico predictions; HDX-MS is well-placed to meet this demand. Here we present a protocol for HDX-MS and illustrate its use in characterizing the dynamics and structural changes of a dimeric heme-containing oxygen sensor protein as it responds to changes in its coordination and redox state. This allowed us to propose a mechanism by which the signal (oxygen binding to the heme iron in the sensing domain) is transduced to the protein's functional domain.


Subject(s)
Hemeproteins , Deuterium , Deuterium Exchange Measurement/methods , Artificial Intelligence , Mass Spectrometry/methods , Hydrogen/chemistry , Oxygen/metabolism , Heme/chemistry
16.
FEBS J ; 290(3): 821-836, 2023 02.
Article in English | MEDLINE | ID: mdl-36062318

ABSTRACT

Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains, and a holistic picture of the full-length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modelling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in-solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration-dependent manner, and its oligomerization is mediated via the positively charged N-terminal microtubule-binding domain. Our findings provide the first insights into the structure of full-length human HDAC6 and can be used as a basis for further research into structure function and physiological studies of this unique deacetylase.


Subject(s)
Histone Deacetylases , Microtubules , Humans , Histone Deacetylase 6/genetics , Histone Deacetylase 6/chemistry , Histone Deacetylase 6/metabolism , Histone Deacetylases/metabolism , Microtubules/metabolism , Histone Deacetylase Inhibitors , Acetylation
17.
Enzyme Microb Technol ; 164: 110187, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36610228

ABSTRACT

The aim of this work was to map the sequence space of aldoxime dehydratases (Oxds) as enzymes with great potential for nitrile synthesis. Microbes contain an abundance of putative Oxds but fewer than ten Oxds were characterized in total and only two in fungi. In this work, we prepared and characterized a new Oxd (protein gb|EEU37245.1 named OxdFv) from Fusarium vanettenii 77-13-4. OxdFv is distant from the characterized Oxds with a maximum of 36% identity. Moreover, the canonical Oxd catalytic triad RSH is replaced by R141-E187-E303 in OxdFv. R141A and E187A mutants did not show significant activities, but mutant E303A showed a comparable activity as the wild-type enzyme. According to native mass spectrometry, OxdFv contained almost 1 mol of heme per 1 mol of protein, and was composed of approximately 88% monomer (41.8 kDa) and 12% dimer. A major advantage of this enzyme is its considerable activity under aerobic conditions (25.0 ± 4.3 U/mg for E,Z-phenylacetaldoxime at pH 9.0 and 55 °C). Addition of sodium dithionite (reducing agent) and Fe2+ was required for this activity. OxdFv favored (aryl)aliphatic aldoximes over aromatic aldoximes. Substrate docking in the homology model of OxdFv showed a similar substrate specificity. We conclude that OxdFv is the first characterized Oxd of the REE type.


Subject(s)
Fusarium , Fusarium/genetics , Hydro-Lyases/genetics , Hydro-Lyases/metabolism , Catalysis , Oximes/metabolism
18.
Methods Mol Biol ; 2247: 193-219, 2021.
Article in English | MEDLINE | ID: mdl-33301119

ABSTRACT

Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein-DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.


Subject(s)
DNA-Binding Proteins/chemistry , DNA/chemistry , Hydrogen Deuterium Exchange-Mass Spectrometry , Animals , Binding Sites , Chromatography, Liquid , DNA/metabolism , DNA-Binding Proteins/metabolism , Data Analysis , Humans , Hydrogen Deuterium Exchange-Mass Spectrometry/methods , Protein Binding , Protein Interaction Domains and Motifs , Transcription Factors
19.
ACS Catal ; 11(2): 517-532, 2021 Jan 15.
Article in English | MEDLINE | ID: mdl-33489432

ABSTRACT

The natural function of cellobiose dehydrogenase (CDH) to donate electrons from its catalytic flavodehydrogenase (DH) domain via its cytochrome (CYT) domain to lytic polysaccharide monooxygenase (LPMO) is an example of a highly efficient extracellular electron transfer chain. To investigate the function of the CYT domain movement in the two occurring electron transfer steps, two CDHs from the ascomycete Neurospora crassa (NcCDHIIA and NcCDHIIB) and five chimeric CDH enzymes created by domain swapping were studied in combination with the fungus' own LPMOs (NcLPMO9C and NcLPMO9F). Kinetic and electrochemical methods and hydrogen/deuterium exchange mass spectrometry were used to study the domain movement, interaction, and electron transfer kinetics. Molecular docking provided insights into the protein-protein interface, the orientation of domains, and binding energies. We find that the first, interdomain electron transfer step from the catalytic site in the DH domain to the CYT domain depends on steric and electrostatic interface complementarity and the length of the protein linker between both domains but not on the redox potential difference between the FAD and heme b cofactors. After CYT reduction, a conformational change of CDH from its closed state to an open state allows the second, interprotein electron transfer (IPET) step from CYT to LPMO to occur by direct interaction of the b-type heme and the type-2 copper center. Chimeric CDH enzymes favor the open state and achieve higher IPET rates by exposing the heme b cofactor to LPMO. The IPET, which is influenced by interface complementarity and the heme b redox potential, is very efficient with bimolecular rates between 2.9 × 105 and 1.1 × 106 M-1 s-1.

20.
J Am Chem Soc ; 132(19): 6800-8, 2010 May 19.
Article in English | MEDLINE | ID: mdl-20420392

ABSTRACT

Pentapeptide diacidic sequence LELTE, derived from the mycobacterial heat shock protein hsp65, has been recently identified as a "danger" signal of the immune system effective via specific binding to the universal leukocyte triggering receptor CD69. This sequence is not active per se, only after its presentation within the multivalent environment of its parent protein, or after artificial dimerization using a standard bifunctional reagents. Here we describe an entirely new way of presenting of this peptide based on its attachment to a cyclopeptide RAFT scaffold (K-K-K-P-G)(2) through the epsilon-amino group of lysine residues, alone or in combination with the carbohydrate epitope alphaGalNAc. The ability of such RAFT scaffolds to precipitate the target CD69 receptor or to activate CD69-positive cells is enhanced in compounds 2 and 4 possessing combined peptide/carbohydrate expression. Compounds 2 and 4 are highly efficient activators of natural killer lymphocytes, but they are completely inactive from the point of view of activation-induced apoptosis of lymphocytes by the target cells. These unique properties make the combined peptide/carbohydrate RAFTs highly suitable for future evaluation in animal tumor therapies in vivo and predict them to be readily available and efficient immunoactivators.


Subject(s)
Glycoconjugates/chemical synthesis , Glycoconjugates/metabolism , Leukocytes, Mononuclear/immunology , Oligopeptides/immunology , Oligopeptides/metabolism , Amino Acid Sequence , Antigens, CD/metabolism , Antigens, Differentiation, T-Lymphocyte/metabolism , Glycoconjugates/chemistry , Glycosylation , Humans , Lectins, C-Type/metabolism , Leukocytes, Mononuclear/metabolism , NK Cell Lectin-Like Receptor Subfamily B/metabolism , Oligopeptides/chemistry , Oximes/chemistry , Peptides, Cyclic/chemistry , Peptides, Cyclic/metabolism
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