Substrate Release Research Articles

Nucleotide exchange factors Fes1 and HspBP1 mimic substrate to release misfolded proteins from Hsp70.

Protein quality control depends on the tight regulation of interactions between molecular chaperones and polypeptide substrates. Substrate release from the chaperone Hsp70 is triggered by nucleotide-exchange factors (NEFs) that control folding and degradation fates via poorly understood mechanisms. We found that the armadillo-type NEFs budding yeast Fes1 and its human homolog HspBP1 employ flexible N-terminal release domains (RDs) with substrate-mimicking properties to ensure the efficient release of persistent substrates from Hsp70. The RD contacts the substrate-binding domain of the chaperone, competes with peptide substrate for binding and is essential for proper function in yeast and mammalian cells. Thus, the armadillo domain engages Hsp70 to trigger nucleotide exchange, whereas the RD safeguards the release of substrates. Our findings provide fundamental mechanistic insight into the functional specialization of Hsp70 NEFs and have implications for the understanding of proteostasis-related disorders, including Marinesco-Sjögren syndrome.

Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter.

Computational evaluation of the energetics of substrate binding, transport, and release events of neurotransmitter transporters at the molecular level is a challenge, as the structural transitions of these membrane proteins involve coupled global and local changes that span time scales of several orders of magnitude, from nanoseconds to seconds. Here, we provide a quantitative assessment of the energetics of dopamine (DA) translocation through the human DA transporter (hDAT), using a combination of molecular modeling, simulation, and analysis tools. DA-binding and -unbinding events, which generally involve local configurational changes, are evaluated using free-energy perturbation or adaptive biasing force methods. The global transitions between the outward-facing state and the inward-facing state, on the other hand, require a dual-boost accelerated molecular dynamics simulation. We present results on DA-binding/unbinding energetics under different conditions, as well as the conformational energy landscape of hDAT in both DA-bound and -unbound states. The study provides a tractable method of approach for quantitative evaluation of substrate-binding energetics and efficient estimation of conformational energy landscape, in general.

The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.

The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a 'conveyor belt' model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end.

Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s

Cellular protein homeostasis depends on heat shock proteins 70 kDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and release. To illuminate the molecular mechanism of this allosteric coupling, here we present a novel crystal structure of an intact human BiP, an essential Hsp70 in ER, in an ATP-bound state. Strikingly, the polypeptide-binding pocket is completely closed, seemingly excluding any substrate binding. Our FRET, biochemical and EPR analysis suggests that this fully closed conformation is the major conformation for the ATP-bound state in solution, providing evidence for an active release of bound polypeptide substrates following ATP binding. The Hsp40 co-chaperone converts this fully closed conformation to an open conformation to initiate productive substrate binding. Taken together, this study provided a mechanistic understanding of the dynamic nature of the polypeptide-binding pocket in the Hsp70 chaperone cycle.

The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains

Hsp70 molecular chaperones play key roles in cellular protein homeostasis by binding to exposed hydrophobic regions of incompletely folded or aggregated proteins. This crucial Hsp70 function relies on allosteric communication between two well-structured domains: an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD), which are tethered by an interdomain linker. ATP or ADP binding to the NBD alters the substrate-binding affinity of the SBD, triggering functionally essential cycles of substrate binding and release. The interdomain linker is a well-structured participant in the interdomain interface in ATP-bound Hsp70s. By contrast, in the ADP-bound state, exemplified by the Escherichia coli Hsp70 DnaK, the interdomain linker is flexible. Hsp70 interdomain linker sequences are highly conserved; moreover, mutations in this region compromise interdomain allostery. To better understand the role of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformational landscape of the interdomain linker in ADP-bound DnaK and supported our simulations by strategic experimental data. We found that while the interdomain linker samples many conformations, it behaves as three relatively ordered segments connected by hinges. As a consequence, the distances and orientations between the NBD and SBD are limited. Additionally, the C-terminal region of the linker forms previously unreported, transient interactions with the SBD, and the predominant linker-docking site is available in only one allosteric state, that with high affinity for substrate. This preferential binding implicates the interdomain linker as a dynamic allosteric switch. The linker-binding site on the SBD is a potential target for small molecule modulators of the Hsp70 allosteric cycle.

Conformations of the HIV-1 protease: A crystal structure data set analysis

The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein.

Transcranial Doppler in autonomic testing: standards and clinical applications.

When cerebral blood flow falls below a critical limit, syncope occurs and, if prolonged, ischemia leads to neuronal death. The cerebral circulation has its own complex finely tuned autoregulatory mechanisms to ensure blood supply to the brain can meet the high metabolic demands of the underlying neuronal tissue. This involves the interplay between myogenic and metabolic mechanisms, input from noradrenergic and cholinergic neurons, and the release of vasoactive substrates, including adenosine from astrocytes and nitric oxide from the endothelium. Transcranial Doppler (TCD) is a non-invasive technique that provides real-time measurements of cerebral blood flow velocity. TCD can be very useful in the work-up of a patient with recurrent syncope. Cerebral autoregulatory mechanisms help defend the brain against hypoperfusion when perfusion pressure falls on standing. Syncope occurs when hypotension is severe, and susceptibility increases with hyperventilation, hypocapnia, and cerebral vasoconstriction. Here we review clinical standards for the acquisition and analysis of TCD signals in the autonomic laboratory and the multiple methods available to assess cerebral autoregulation. We also describe the control of cerebral blood flow in autonomic disorders and functional syndromes.

Toward an understanding of the Cdc48/p97 ATPase.

A conserved AAA+ ATPase, called Cdc48 in yeast and p97 or VCP in metazoans, plays an essential role in many cellular processes by segregating polyubiquitinated proteins from complexes or membranes. For example, in endoplasmic reticulum (ER)-associated protein degradation (ERAD), Cdc48/p97 pulls polyubiquitinated, misfolded proteins out of the ER and transfers them to the proteasome. Cdc48/p97 consists of an N-terminal domain and two ATPase domains (D1 and D2). Six Cdc48 monomers form a double-ring structure surrounding a central pore. Cdc48/p97 cooperates with a number of different cofactors, which bind either to the N-terminal domain or to the C-terminal tail. The mechanism of Cdc48/p97 action is poorly understood, despite its critical role in many cellular systems. Recent in vitro experiments using yeast Cdc48 and its heterodimeric cofactor Ufd1/Npl4 (UN) have resulted in novel mechanistic insight. After interaction of the substrate-attached polyubiquitin chain with UN, Cdc48 uses ATP hydrolysis in the D2 domain to move the polypeptide through its central pore, thereby unfolding the substrate. ATP hydrolysis in the D1 domain is involved in substrate release from the Cdc48 complex, which requires the cooperation of the ATPase with a deubiquitinase (DUB). Surprisingly, the DUB does not completely remove all ubiquitin molecules; the remaining oligoubiquitin chain is also translocated through the pore. Cdc48 action bears similarities to the translocation mechanisms employed by bacterial AAA ATPases and the eukaryotic 19S subunit of the proteasome, but differs significantly from that of a related type II ATPase, the NEM-sensitive fusion protein (NSF). Many questions about Cdc48/p97 remain unanswered, including how it handles well-folded substrate proteins, how it passes substrates to the proteasome, and how various cofactors modify substrates and regulate its function.

Effect of repeated drying–rewetting cycles on microbial biomass carbon in soils with different climatic histories

There are contrasting results regarding the effect of repeated drying–rewetting (DRW) cycles on microbial biomass carbon (MBC), and two fundamentally different mechanisms have been postulated. The first is a microbial stress mechanism which will reduce MBC as stress-sensitive microbes die, and the second is a substrate supply mechanism which will increase MBC through the release of a microbial substrate from non-biomass soil organic carbon (C). However, the balance of these two mechanisms has not been fully examined for various soils with different climatic histories, especially for soils from humid areas. We hypothesized that soils subjected to fewer DRW events would be largely affected by the stress mechanism. Therefore, the effect of repeated DRW cycles on MBC and C dynamics was investigated and compared to that of a moist control treatment for four soils with different DRW histories. The first DRW significantly reduced the MBC for soils with less DRW but not for soils with more DRW. However, when comparing the sizes of MBC after 28days of four DRW cycles and the moist treatment, the result was not related to the microbial resistance of each DRW. Cumulative respired CO2-C over a 4-day moist period after each DRW was always significantly greater than that in the moist treatment even when the MBC was not reduced by the DRW. The results with no change in MBC suggested that the substrate supply mechanism rather than the stress mechanism would be essential for the effect of repeated DRW cycles on MBC and C dynamics.

Systematic evaluation of characteristics of the membrane-based fed-batch shake flask

BackgroundThe initial part of process development involves extensive screening programs to identify optimal biological systems and cultivation conditions. For a successful scale-up, the operation mode on screening and production scale must be as close as possible. To enable screening under fed-batch conditions, the membrane-based fed-batch shake flask was developed. It is a shake flask mounted with a central feed reservoir with an integrated rotating membrane tip for a controlled substrate release. Building on the previously provided proof of principle for this tool, this work extends its application by constructive modifications and improved methodology to ensure reproducible performance.ResultsThe previously limited operation window was expanded by a systematic analysis of reservoir set-up variations for cultivations with the fast-growing organism Escherichia coli. Modifying the initial glucose concentration in the reservoir as well as interchanging the built-in membrane, resulted in glucose release rates and oxygen transfer rate levels during the fed-batch phase varying up to a factor of five. The range of utilizable membranes was extended from dialysis membranes to porous microfiltration membranes with the design of an appropriate membrane tip. The alteration of the membrane area, molecular weight cut-off and liquid volume in the reservoir offered additional parameters to fine-tune the duration of the initial batch phase, the oxygen transfer rate level of the fed-batch phase and the duration of feeding. It was shown that a homogeneous composition of the reservoir without a concentration gradient is ensured up to an initial glucose concentration of 750 g/L. Finally, the experimental validity of fed-batch shake flask cultivations was verified with comparable results obtained in a parallel fed-batch cultivation in a laboratory-scale stirred tank reactor.ConclusionsThe membrane-based fed-batch shake flask is a reliable tool for small-scale screening under fed-batch conditions filling the gap between microtiter plates and scaled-down stirred tank reactors. The implemented reservoir system offers various set-up possibilities, which provide a wide range of process settings for diverse biological systems. As a screening tool, it accurately reflects the cultivation conditions in a fed-batch stirred tank reactor and enables a more efficient bioprocess development.

Rational Engineering of a Dynamic, Entropy-Driven DNA Nanomachine for Intracellular MicroRNA Imaging.

We rationally engineered an elegant entropy-driven DNA nanomachine with three-dimensional track and applied it for intracellular miRNAs imaging. The proposed nanomachine is activated by target miRNA binding to drive a walking leg tethered to gold nanoparticle with a high density of DNA substrates. The autonomous and progressive walk on the DNA track via the entropy-driven catalytic reaction of intramolecular toehold-mediated strand migration leads to continuous disassembly of DNA substrates, accompanied by the recovery of fluorescence signal due to the specific release of a dye-labeled substrate from DNA track. Our nanomachine outperforms the conventional intermolecular reaction-based gold nanoparticle design in the context of an improved sensitivity and kinetics, attributed to the enhanced local effective concentrations of working DNA components from the proximity-induced intramolecular reaction. Moreover, the nanomachine was applied for miRNA imaging inside living cells.

Electron crystallography reveals that substrate release from the PTS IIC glucose transporter is coupled to a subtle conformational change.

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIICglc) to visualize the structure of the transporter in the presence and absence of its substrate. Using an in vivo transport assay and binding competition experiments, we first established that, while it transports d-glucose, ecIICglc does not bind l-glucose. We then determined the projection structure of ecIICglc from tubular crystals embedded in d- and l-glucose and found a subtle conformational change. From comparison of the ecIICglc projection maps with crystal structures of other IIC transporters, we can deduce that the transporter adopts an inward-facing conformation, and that the maps in the presence and absence of the substrate reflect the transporter before and after release of the transported glucose into the cytoplasm. The transition associated with substrate release appears to require a subtle structural rearrangement in the region that includes hairpin 1.

Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex

The Cdc48 ATPase and its cofactors Ufd1/Npl4 (UN) extract polyubiquitinated proteins from membranes or macromolecular complexes, but how they perform these functions is unclear. Cdc48 consists of an N-terminal domain that binds UN and two stacked hexameric ATPase rings (D1 and D2) surrounding a central pore. Here, we use purified components to elucidate how the Cdc48 complex processes substrates. After interaction of the polyubiquitin chain with UN, ATP hydrolysis by the D2 ring moves the polypeptide completely through the double ring, generating a pulling force on the substrate and causing its unfolding. ATP hydrolysis by the D1 ring is important for subsequent substrate release from the Cdc48 complex. This release requires cooperation of Cdc48 with a deubiquitinase, which trims polyubiquitin to an oligoubiquitin chain that is then also translocated through the pore. Together, these results lead to a new paradigm for the function of Cdc48 and its mammalian ortholog p97/VCP.

The Mechanism of Inhibition of Botulinum Neurotoxin Type A by Two Quinolinol Compounds

The potential of Botulinum neurotoxins (BoNTs) to be used as biological weapons makes the need to identify small molecule inhibitors critical but it is a challenging target due to the large substrate‐enzyme interface. BoNTs are produced by the bacterium Clostridium botulinum in seven antigenically distinct serotypes (A‐G), with serotype A (BoNT/A) being the most potent toxin known to man. Recently, quinolinol‐based compounds have been identified as a promising starting point for effective BoNT/A inhibitors. Understanding the mechanism of inhibition by quinolinol compounds would facilitate inhibitor optimization studies. In this study, a Foster resonance energy transfer (FRET) based substrate of BoNT/A, SNAPtide, was used to study the mechanism of inhibition of BoNT/A endopeptidase activity by two new quinolinol compounds, MSU58 and MSU84, with IC50 values of 3.3 μM and 5.8 μM, respectively. Kinetic analysis and model discrimination analysis revealed both compounds to be competitive inhibitors of BoNT/A endopeptidase activity. Inhibition constants (KI) were found to be 3.2 μM for MSU58 and 6.2 μM for MSU84. The kinetic rate constant for the binding and release of substrate and inhibitor were also determined. These data indicate that these inhibitors bind in the active site of BoNT/A and that binding is mutually exclusive with the binding of the substrate. This study, is the first to report on the competitive inhibition of BoNT/A by a quinolinol group of compounds. These data help define the inhibitor binding pocket and, along with structure activity relationship studies, provide immediate direction for further compound synthesis.Support or Funding InformationNovartis Graduate Scholarship Award and US Army Medical Research (grant number W81XWH‐14‐C‐0090 S)

Polycyclic Aromatic Hydrocarbons as Sublimable Adhesives

Polycyclic aromatic hydrocarbons (PAHs) are used as adhesives that can be removed on-demand by sublimation without application of solvent or mechanical force. These adhesives are polycrystalline solids that enable bonding of glass, metal, and plastic with lap shear forces ranging from 5 to 50 N cm–2. Systematic examination of factors governing bonding suggests that favorable chemical interactions between bonded surfaces and PAHs, and structural features at the surface of the substrate influence both the lap shear force and the mechanism of failure. Utilizing sublimable PAHs enables sequential bonding and release of substrates, as well as control of actuation of electronic systems through mechanical work.

Novel thermoresponsive water-soluble oligomers based on amphiphilic calixresorcinarenes

Novel water-soluble thermoresponsive oligomers TO1 and TO2 were obtained by reaction of amidoamine tetramethylcalixresorcinarenes (C1) and tetrapentylcalixresorcinarenes (C5) with ethylene glycol diglycidyl ether. The compounds were characterised by 1H and FT-PGSE NMR, FTIR, static light scattering and elemental analysis. The thermoresponsive properties of oligomers were investigated by spectrophotometry, DLS, FT-PGSE NMR and TEM. The cloud points of oligomers (43 °C for TO1 (5 mg/ml) and 41 °C for TO2 (1.2 mg/ml), respectively) were determined. The influence of salts effect on TO2 cloud points was investigated. The binding of anti-inflammatory drug naproxen (Nap) at 20 °C by TO1 and TO2 and its partial release at cloud points of oligomers in aqueous solution are observed using fluorescence and FT-PGSE NMR methods. New example of creating of thermoresponsive macrocyclic systems on the basis of amidoamine calixresorcinarenes with possibility of substrate binding and release under the influence of termo-stimuli in an aqueous solution was shown.

Hsp70 displaces small heat shock proteins from aggregates to initiate protein refolding.

Small heat shock proteins (sHsps) are an evolutionary conserved class of ATP-independent chaperones that protect cells against proteotoxic stress. sHsps form assemblies with aggregation-prone misfolded proteins, which facilitates subsequent substrate solubilization and refolding by ATP-dependent Hsp70 and Hsp100 chaperones. Substrate solubilization requires disruption of sHsp association with trapped misfolded proteins. Here, we unravel a specific interplay between Hsp70 and sHsps at the initial step of the solubilization process. We show that Hsp70 displaces surface-bound sHsps from sHsp-substrate assemblies. This Hsp70 activity is unique among chaperones and highly sensitive to alterations in Hsp70 concentrations. The Hsp70 activity is reflected in the organization of sHsp-substrate assemblies, including an outer dynamic sHsp shell that is removed by Hsp70 and a stable core comprised mainly of aggregated substrates. Binding of Hsp70 to the sHsp/substrate core protects the core from aggregation and directs sequestered substrates towards refolding pathway. The sHsp/Hsp70 interplay has major impact on protein homeostasis as it sensitizes substrate release towards cellular Hsp70 availability ensuring efficient refolding of damaged proteins under favourable folding conditions.

Mechanistic Insights into Outer Membrane Protein Folding

The beta-barrel outer membrane proteins (OMPs) of Gram-negative bacteria are essential for cell viability and survival, but the molecular mechanisms of their biogenesis remain poorly understood. OMPs are synthesised in the cytoplasm, translocated across the inner membrane and transported across the periplasm by the molecular chaperones Skp or SurA, before being inserted into the OM by the essential beta-barrel assembly machinery (BAM) complex (a 203 kDa heteropentameric membrane protein complex). The mechanisms by which Skp and SurA recognise OMPs and successfully deliver their cargos to BAM remain poorly understood. Questions about these mechanisms are especially interesting since the periplasm is devoid of ATP, and it is completely unknown how substrate binding and release are controlled and coordinated. Moreover, whilst several structures of the BAM complex have been solved recently, how OMPs are delivered to BAM from Skp/SurA and folded into the crowded outer membrane remain mysterious. We have been exploiting a range of biophysical methods to gain new insights into the mechanisms of OMP folding and assembly, and its assistance by chaperones and BAM. In this lecture I will describe our recent results using a variety of OMPs of different sizes combined with analysis using fluorescence kinetic assays, cryo-EM and non-covalent mass spectrometry. The results have revealed a new mechanism of Skp action and new insights into how BAM facilitates OMP folding into the bacterial outer membrane.

Methane Emission Potential from Freshwater Marsh Soils of Northeast China: Response to Simulated Freezing-Thawing Cycles

Boreal wetlands are significant natural sources of methane (CH4) to the atmosphere, and are vulnerable to freezing-thawing cycles (FTC). Nonetheless, the underlying factors that induce CH4 emission in boreal wetlands during FTC are still unclear. Our goal was to characterize soil CH4 emission potential from a freshwater marsh as impacted by FTC and to determine the corresponding mechanisms. We collected soil samples from two soil layers (0–20 and 20–40 cm) of an undisturbed freshwater marsh in Sanjiang Plain, Northeast China, and subjected them to various freezing (6 to −6 °C) and thawing (−6 to 6 °C) cycles. Soil CH4 emission, DOC, and the aromaticity and complexity of DOC indexes were monitored. The results showed that FTC significantly increased CH4 emission potential in the 0–20 cm surface soil layer. The maximum hourly CH4 emission rate was 55.0 mg C m−2 h−1, approximately 19 times as high as that of the unfrozen control sample (2.8 mg C m−2 h−1). However, the peak intensity of CH4 emission decreased when the numbers of FTC increased. Meanwhile, FTC not only increased the quantity of DOC released, but also enhanced its instability via increasing the contribution of relatively small, readily degradable organic molecules. Additionally, the CH4 emission potential was significantly correlated with the aromaticity and complexity of DOC, indicating that the release of labile substrates under FTC was one important factor controlling the microbial production of CH4 and the high emissions upon thawing. Our study suggested that global warming-induced increases in seasonal FTC in boreal wetlands may increase CH4 emissions beyond what would occur from long-term temperature increases alone.

FRET-based characterization of K264A, D345A, and Y335Amutants in the human dopamine transporter

The dopamine transporter (DAT) plays a role in the termination of dopaminergic neurotransmission; thereby it is accepted as the primary target of various psychostimulants. N-terminal phosphorylation of DAT has been proposed as a regulator in different DAT functions, such as amphetamine-induced efflux or PKC/PKA-mediated responses. To understand the role of N-terminal conformational changes in dopamine transporter structure and function, the fluorescence resonance energy transfer (FRET) method was applied to various DAT constructs fluorescently labeled at the N-terminus and substrate-induced conformational changes were determined using rhodamine-labeled cocaine analog JHC1-64 in three DAT mutants. The results indicated that the construct with YFP inserted into the N-terminal position-55 displayed effective interaction with the substrate and simultaneous mutation of two serine residues (S7 and S12) to alanine or aspartic acid demonstrated similar phenotypes as their wild-type (WT) counterparts. FRET was detectable for N-terminal p55 YFP WT, Ser/Ala, and Ser/Asp forms, but there was no significant difference among the three mutants, contrary to our expectations based on the previously proposed roles of these serine residues. In addition, three mutants (K264A, D345A, and Y335A) implemented in the position-55 YFP background were also investigated and the importance of Y335 in the translocation cycle and in the process of substrate release was verified.