Refolding of denatured/reduced lysozyme at high concentrations by artificial molecular chaperone‐ion exchange chromatography

Development of high efficiency and low cost protein refolding methods is a highlighted research focus in biotechnology. Artificial molecular chaperone (AMC) and protein folding liquid chromatography (PFLC) are two attractive refolding methods developed in recent years. In the present work, AMC and one branch of PFLC, ion exchange chromatography (IEC), are integrated to form a new refolding method, artificial molecular chaperone‐ion exchange chromatography (AMC‐IEC). This new method is applied to the refolding of a widely used model protein, urea‐denatured/dithiothreitol‐reduced lysozyme. Many factors influencing the refolding of lysozyme, such as urea concentration, β‐cyclodextrin concentration, molar ratio of detergent to protein, mobile phase flow rate, and type of detergent, were investigated, respectively, to optimize the conditions for lysozyme refolding by AMC‐IEC. Compared with normal IEC refolding method, the activity recoveries of lysozyme obtained by AMC‐IEC were much higher in the investigated range of initial protein concentrations. Moreover, the activity recoveries obtained by using this newly developed refolding method were still quite high for denatured/reduced lysozyme at high initial concentrations. When the initial protein concentration was 200 mg mL^?1, the activity recovery was over 60%. In addition, the lifetime of the chromatographic column during AMC‐IEC was much longer than that during protein refolding by normal IEC. Therefore, AMC‐IEC is a high efficient and low cost protein refolding method. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

GTP‐dependent permeabilized neutrophil secretion requires a freely diffusible cytosolic protein

Guanosine triphosphate (GTP) has been implicated in the regulation of Ca²⁺‐mediated secretion from neutrophils. We further examined the role of GTP in neutrophil secretion using streptolysin O permeabilized cells. We found that, in the presence of GTP, 1.0 μM free Ca²⁺ causes maximum secretion—equivalent to that achieved with 100 μM free Ca²⁺—whereas GTPγS inhibits Ca²⁺‐stimulated secretion. Interestingly, GTP by itself stimulates secretion. These results indicate the existence of a GTP‐regulated mechanism of secretion in neutrophils that requires GTP hydrolysis to stimulate secretion in the presence and absence of Ca²⁺. The stimulatory effect of GTP is only observed when GTP is present during permeabilization. Addition of GTP after permeabilization, when the cytosolic contents have leaked out from cells, gives no stimulatory response, implying that the GTP‐dependent secretory apparatus requires at least one cytosolic protein. GTP‐dependent secretion can be reconstituted with crude HL‐60 and bovine liver cytosol. The reconstituting activity binds to GTP‐agarose, suggesting that the cytosolic factor is a GTP‐binding protein or forms a complex with a GTP‐binding protein. However, it is not a member of the rho or rac families of GTPases. By gel filtration chromatography, the secretion‐reconstituting activity eluted at 870 and 200 kDa, but in the presence of GTP, eluted at 120 kDa, indicating that it is part of a high‐molecular‐weight complex that dissociates in the presence of GTP. Retention of adenosine diphosphate‐ribosylation factor (ARF) in permeabilized cells and insensitivity of the cytosolic reconstituting activity to brefeldin A led to our speculation that ARF6 may be the GTPase involved in GTP‐dependent secretion, and that activity from a BFA‐insensitive ARF6 guanine nucleotide exchange factor reconstitutes secretion. J. Cell. Biochem. 80:37–45, 2000. © 2000 Wiley‐Liss, Inc.     

A direct role for phosphatidylinositol-4,5-bisphosphate in unconventional secretion of fibroblast growth factor 2

Fibroblast growth factor 2 (FGF-2) is a mitogen that is exported from cells by an endoplasmic reticulum/Golgi-independent secretory pathway. Recent findings have shown that FGF-2 export occurs by direct translocation from the cytoplasm across the plasma membrane into the extracellular space. Here, we report that FGF-2 contains a binding site for phosphatidylinositol-4,5-bisphosphate [PI(4,5)P₂], the principal phosphoinositide species associated with plasma membranes. Intriguingly, in the context of a lipid bilayer, the interaction between FGF-2 and PI(4,5)P₂ is shown to depend on a lipid background that resembles plasma membranes. We show that the interaction with PI(4,5)P₂ is critically important for FGF-2 secretion as experimental conditions reducing cellular levels of PI(4,5)P₂ resulted in a substantial drop in FGF-2 export efficiency. Likewise, we have identified FGF-2 variant forms deficient for binding to PI(4,5)P₂ that were found to be severely impaired with regard to export efficiency. These data show that a transient interaction with PI(4,5)P₂ associated with the inner leaflet of plasma membranes represents the initial step of the unconventional secretory pathway of FGF-2.     

An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress

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Tec‐Kinase‐Mediated Phosphorylation of Fibroblast Growth Factor 2 is Essential for Unconventional Secretion

Fibroblast growth factor 2 (FGF2) is a potent mitogen that is exported from cells by an endoplasmic reticulum (ER)/Golgi‐independent mechanism. Unconventional secretion of FGF2 occurs by direct translocation across plasma membranes, a process that depends on the phosphoinositide phosphatidylinositol 4,5‐biphosphate (PI(4,5)P₂) at the inner leaflet as well as heparan sulfate proteoglycans at the outer leaflet of plasma membranes; however, additional core and regulatory components of the FGF2 export machinery have remained elusive. Here, using a highly effective RNAi screening approach, we discovered Tec kinase as a novel factor involved in unconventional secretion of FGF2. Tec kinase does not affect FGF2 secretion by an indirect mechanism, but rather forms a heterodimeric complex with FGF2 resulting in phosphorylation of FGF2 at tyrosine 82, a post‐translational modification shown to be essential for FGF2 membrane translocation to cell surfaces. Our findings suggest a crucial role for Tec kinase in regulating FGF2 secretion under various physiological conditions and, therefore, provide a new perspective for the development of a novel class of antiangiogenic drugs targeting the formation of the FGF2/Tec complex.     

Improved secretion of molecular chaperone‐assisted human IgG in silkworm,and no alterations in their N‐linked glycan structures

Human 29IJ6 IgG was expressed in silkworm using a Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid system. The mean amounts of 296IJ6 IgG produced in larval hemolymph and whole pupae were 30.1 μg/larva and 78.0 μg/pupa, respectively. The use of molecular chaperones including calreticulin (CRT), calnexin (CNX), and immunoglobulin heavy chain binding protein (BiP, GRP78) improved the production of 296IJ6 IgG secretion in the larvae fivefold. The total yield of recombinant 29IJ6 IgG was 239 μg/mL when coexpressed with CRT. However, the overexpression of molecular chaperones had negative effects on secretion. The N‐linked glycans of secreted 296IJ6 IgG in silkworm hemolymph were dominated by paucimannose structures. Small amounts of GlcNAc residues linked to the Manα1,3 branch were detected. When molecular chaperones were coexpressed, the compositions of N‐linked glycans in the IgG1 produced were unchanged compared with those produced without them. This suggests that N‐glycosylation is controlled by a regulatory function in the Golgi apparatus even though the post‐translational modification of 296IJ6 IgG was assisted by the coexpression of molecular chaperones. Therefore, if the glycosylation pathways that coexpress N‐acetylglucosaminyltransferase, galactosyltransferase, and sialyltransferase could be improved, silkworm larvae might prove a useful system for producing human antibodies. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin reveal a highly extended chain architecture

The covalent attachment of different types of poly‐ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys‐48‐linked poly‐ubiquitin chains is targeted for proteasomal degradation, whereas Lys‐63‐linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X‐ray crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin at resolutions of 2.3 and 1.9 Å, respectively. The tri‐ and di‐ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left‐handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of ～110 Å. Interestingly, Lys‐48 ubiquitin chains also adopt a left‐handed helical structure with a similar repeat length. However, the Lys‐63 architecture is much more open than that of Lys‐48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys‐63 chain conformation, and reveal the structural basis for differential recognition of Lys‐63 versus Lys‐48 chains. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture

Fertilization triggers assembly of higher‐order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single‐nucleus Hi‐C (snHi‐C), but not bulk Hi‐C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin‐dependent loop extrusion generates higher‐order chromatin structures within the one‐cell embryo. Using snHi‐C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1‐cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi‐C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin‐dependent loop extrusion organizes mammalian genomes over multiple scales from the one‐cell embryo onward.     

Conformational and aggregation properties of the 1–93 fragment of apolipoprotein A‐I

Several disease‐linked mutations of apolipoprotein A‐I, the major protein in high‐density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N‐terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril‐associated disordered 1–93 fragment of this protein, in wild‐type and mutated (G26R, S36A, K40L, W50R) forms. In atomic‐level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position‐dependent β‐strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease‐linked aggregation of apolipoprotein A‐I.     

Activity‐dependent release of tissue plasminogen activator from the dendritic spines of hippocampal neurons revealed by live‐cell imaging

Tissue plasminogen activator (tPA) has been implicated in a variety of important cellular functions, including learning‐related synaptic plasticity and potentiating N‐methyl‐D ‐aspartate (NMDA) receptor‐dependent signaling. These findings suggest that tPA may localize to, and undergo activity‐dependent secretion from, synapses; however, conclusive data supporting these hypotheses have remained elusive. To elucidate these issues, we studied the distribution, dynamics, and depolarization‐induced secretion of tPA in hippocampal neurons, using fluorescent chimeras of tPA. We found that tPA resides in dense‐core granules (DCGs) that traffic to postsynaptic dendritic spines and that can remain in spines for extended periods. We also found that depolarization induced by high potassium levels elicits a slow, partial exocytotic release of tPA from DCGs in spines that is dependent on extracellular Ca⁺² concentrations. This slow, partial release demonstrates that exocytosis occurs via a mechanism, such as fuse‐pinch‐linger, that allows partial release and reuse of DCG cargo and suggests a mechanism that hippocampal neurons may rely upon to avoid depleting tPA at active synapses. Our results also demonstrate release of tPA at a site that facilitates interaction with NMDA‐type glutamate receptors, and they provide direct confirmation of fundamental hypotheses about tPA localization and release that bear on its neuromodulatory functions, for example, in learning and memory. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006     

ESCRT‐dependent protein sorting is required for the viability of yeast clathrin‐mediated endocytosis mutants

Endocytosis regulates many processes, including signaling pathways, nutrient uptake, and protein turnover. During clathrin‐mediated endocytosis (CME), adaptors bind to cytoplasmic regions of transmembrane cargo proteins, and many endocytic adaptors are also directly involved in the recruitment of clathrin. This clathrin‐associated sorting protein family includes the yeast epsins, Ent1/2, and AP180/PICALM homologs, Yap1801/2. Mutant strains lacking these four adaptors, but expressing an epsin N‐terminal homology (ENTH) domain necessary for viability (4Δ+ENTH), exhibit endocytic defects, such as cargo accumulation at the plasma membrane (PM). This CME‐deficient strain provides a sensitized background ideal for revealing cellular components that interact with clathrin adaptors. We performed a mutagenic screen to identify alleles that are lethal in 4Δ+ENTH cells using a colony‐sectoring reporter assay. After isolating candidate synthetic lethal genes by complementation, we confirmed that mutations in VPS4 led to inviability of a 4Δ+ENTH strain. Vps4 mediates the final step of endosomal sorting complex required for transport (ESCRT)‐dependent trafficking, and we found that multiple ESCRTs are also essential in 4Δ+ENTH cells, including Snf7, Snf8 and Vps36. Deletion of VPS4 from an end3Δ strain, another CME mutant, similarly resulted in inviability, and upregulation of a clathrin‐independent endocytosis pathway rescued 4Δ+ENTH vps4Δ cells. Loss of Vps4 from an otherwise wild‐type background caused multiple cargoes to accumulate at the PM because of an increase in Rcy1‐dependent recycling of internalized protein to the cell surface. Additionally, vps4Δ rcy1Δ mutants exhibited deleterious growth phenotypes. Together, our findings reveal previously unappreciated effects of disrupted ESCRT‐dependent trafficking on endocytic recycling and the PM.     

Mechanistic studies of the apical sodium‐dependent bile acid transporter

In mammals, the apical sodium‐dependent bile acid transporter (ASBT) is responsible for the reuptake of bile acid from the intestine, thus recycling bile acid that is secreted from the gallbladder, for the purpose of digestion. As bile acid is synthesized from cholesterol, ASBT inhibition could have important implications in regulation of cholesterol levels in the blood. We report on a simulation study of the recently resolved structures of the inward‐facing ASBT from Neisseria meningitidis and from Yersinia frederiksenii, as well as of an ASBT variant from Yersinia frederiksenii suggested to be in the outward‐facing conformation. Classical and steered atomistic simulations and comprehensive potential of mean force analyses of ASBT, both in the absence and presence of ions and substrate, allow us to characterize and gain structural insights into the Na⁺ binding sites and propose a mechanistic model for the transport cycle. In particular, we investigate structural features of the ion translocation pathway, and suggest a third putative Na⁺ binding site. Our study sheds light on the structure–function relationship of bacterial ASBT and may promote a deeper understanding of transport mechanism altogether. Proteins 2015; 83:1107–1117. © 2015 Wiley Periodicals, Inc.     

Optimized distance‐dependent atom‐pair‐based potential DOOP for protein structure prediction

The DOcking decoy‐based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance‐dependent atom‐pair interactions. To optimize the atom‐pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand–receptor systems (or just pairs). Thus, a total of 8609 ligand–receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand–receptor systems, 1000 evenly sampled docking decoys with 0–10 Å interface root‐mean‐square‐deviation (iRMSD) were generated with a method used before for protein–protein docking. A neural network‐based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel‐like energy landscape for the interaction between these hypothetical ligand–receptor systems. Thus, our method hierarchically models the overall funnel‐like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom‐pair‐based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation‐dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand–receptor systems and their decoys are freely available at http://agknapp.chemie.fu‐berlin.de/doop/ . Proteins 2015; 83:881–890. © 2015 Wiley Periodicals, Inc.