Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and 'aggresomes' during oxidative stress, aging, and disease

Protein aggregation seems to be a common feature of several neurodegenerative diseases and to some extent of physiological aging. It is not always clear why protein aggregation takes place, but a disturbance in the homeostasis between protein synthesis and protein degradation seems to be important. The result is the accumulation of modified proteins, which tend to form high molecular weight aggregates. Such aggregates are also called inclusion bodies, plaques, lipofuscin, ceroid, or ‘aggresomes’ depending on their location and composition. Such aggregates are not inert metabolic end products, but actively influence the metabolism of cells, in particular proteasomal activity and protein turnover. In this review we focus on the influence of oxidative stress on protein turnover, protein aggregate formation and the various interactions of protein aggregates with the proteasome. Furthermore, the formation and effects of protein aggregates during aging and neurodegeneration will be highlighted.     

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information

Protein function is mediated by different amino acid residues, both their positions and types, in a protein sequence. Some amino acids are responsible for the stability or overall shape of the protein, playing an indirect role in protein function. Others play a functionally important role as part of active or binding sites of the protein. For a given protein sequence, the residues and their degree of functional importance can be thought of as a signature representing the function of the protein. We have developed a combination of knowledge- and biophysics-based function prediction approaches to elucidate the relationships between the structural and the functional roles of individual residues and positions. Such a meta-functional signature (MFS), which is a collection of continuous values representing the functional significance of each residue in a protein, may be used to study proteins of known function in greater detail and to aid in experimental characterization of proteins of unknown function. We demonstrate the superior performance of MFS in predicting protein functional sites and also present four real-world examples to apply MFS in a wide range of settings to elucidate protein sequence-structure-function relationships. Our results indicate that the MFS approach, which can combine multiple sources of information and also give biological interpretation to each component, greatly facilitates the understanding and characterization of protein function.     

Protein compressibility, dynamics, and pressure

The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure.     

Circadian formation of clock protein complexes by KaiA,KaiB, KaiC,and SasA in cyanobacteria

Physical interactions among clock-related proteins KaiA, KaiB, KaiC, and SasA are proposed to be important for circadian function in the cyanobacterium Synechococcus elongatus PCC 7942. Here we show that the Kai proteins and SasA form heteromultimeric protein complexes dynamically in a circadian fashion. KaiC forms protein complexes of approximately 350 and 400-600 kDa during the subjective day and night, respectively, and serves as a core of the circadian protein complexes. This change in the size of the KaiC-containing complex is accompanied by nighttime-specific interaction of KaiA and KaiB with KaiC. In various arrhythmic mutants that lack each functional Kai protein or SasA, circadian rhythms in formation of the clock protein complex are abolished, and the size of the protein complexes is dramatically affected. Thus, circadian-regulated formation of the clock protein complexes is probably a critical process in the generation of circadian rhythm in cyanobacteria.     

Cover Image,Volume 87, Issue 7

Template-based modeling is considered as one of the most successful approaches for protein structure prediction. However, reliably and accurately selecting optimal template proteins from a library of known protein structures having similar folds as the target protein and making correct alignments between the target sequence and the template structures, a template-based modeling technique known as threading, remains challenging, particularly for non- or distantly-homologous protein targets. With the recent advancement in protein residue-residue contact map prediction powered by sequence co-evolution and machine learning, here we systematically analyze the effect of inclusion of residue-residue contact information in improving the accuracy and reliability of protein threading. We develop a new threading algorithm by incorporating various sequential and structural features, and subsequently integrate residue-residue contact information as an additional scoring term for threading template selection. We show that the inclusion of contact information attains statistically significantly better threading performance compared to a baseline threading algorithm that does not utilize contact information when everything else remains the same. Experimental results demonstrate that our contact based threading approach outperforms popular threading method MUSTER, contact-assisted ab initio folding method CONFOLD2, and recent state-of-the-art contact-assisted protein threading methods EigenTHREADER and map_align on several benchmarks. Our study illustrates that the inclusion of contact maps is a promising avenue in protein threading to ultimately help to improve the accuracy of protein structure prediction.     

Phosphorylation of a bacterial activator protein, OmpR, by a protein kinase, EnvZ, results in stimulation of its DNA-binding ability

The Escherichia coli OmpR protein is an activator protein specific for the ompF and ompC genes, which respectively encode the outer membrane proteins, OmpF and OmpC. The EnvZ protein is a protein kinase specific for the OmpR protein. In this study, we compared the in vitro DNA-binding ability of the phosphorylated form of the OmpR protein with that of the non-phosphorylated form by means of non-denaturing gel retardation analysis and DNase I footprinting analysis. The results indicate that the phosphorylation of the OmpR protein results in stimulation of its in vitro DNA-binding ability as to both the ompF and ompC promoter DNAs.     

Enhanced protein stability through minimally invasive,direct, covalent,and site‐specific immobilization

Bioconjugating protein to nonbiological surfaces is an essential component of many promising biotechnologies impacting diverse applications such as medical diagnostics, biocatalysis, biohazard detection, and proteomics. However, to enable the widespread economical use of immobilized‐protein technologies, long‐term stability, and reusability is essential. To enhance protein stability in harsh conditions, herein we report a minimally invasive and covalent bioconjugation that enables precise control of the immobilization location at potentially any surface‐accessible location where the incorporated unnatural amino acid does not impact protein structure and function. Specifically, the PRECISE system is introduced where a uniquely reactive unnatural amino acid was incorporated site‐specifically at a prespecified location in GFP using cell‐free protein synthesis. The GFP was then directly and covalently attached to superparamagnetic beads by the unnatural amino acid in a single click reaction. The immobilized GFP was probed for retained activity and stability under harsh conditions including freeze‐thaw cycling and incubation in urea at elevated temperatures. The immobilized GFP was more stable compared to unattached protein in all cases and for all durations observed. The enhanced stability of the immobilized protein is a promising step towards long‐term protein stability for biocatalysis and other immobilized‐protein applications. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

LBL, a novel, developmentally regulated, laminin-binding lectin.

A 190/220-kDa complex found in integrin preparations was purified, and monoclonal antibodies were raised against it. The immunoaffinity-purified complex appears to be a trimer of very similar or identical 70-kDa subunits. It is a novel extracellular matrix molecule as determined by its subunit composition, N-terminal amino acid sequence, and in vivo localization. It is distributed widely in basement membranes including those from muscle, nerve, and kidney. It is also present in connective tissue regions such as perineurium and perimysium. It has the unusual property that it is initially expressed very late in avian development near the time of hatching. This protein is found to copurified with integrin because it binds to the carbohydrate support in Sepharose. Hemagglutination assays with mono- and disaccharides show that it functions as a lectin with galactoside-binding specificity. This protein is also found to bind strongly and specifically to laminin at a site distinct from its lectin activity, but does not bind to fibronectin or type IV collagen. The protein appears to be conserved and is a common contaminant of many laminin preparations. We call this novel protein "LBL" for laminin-binding lectin.     

Fyn binding protein, Fyb, interacts with mammalian actin binding protein, mAbp1

The immune cell specific protein Fyn-T binding protein (Fyb) has been identified as a target of the Yersinia antiphagocytic effector Yersinia outer protein H (YopH), but its role in macrophages is unknown. By using Fyb domains as bait to screen a mouse lymphoma cDNA library, we identified a novel interaction partner, mammalian actin binding protein 1 (mAbp1). We show that mAbp1 binds the Fyb N-terminal via its C-terminally located src homology 3 domain. The interaction between Fyb and mAbp1 is detected in macrophage lysates and the proteins co-localize with F-actin in the leading edge. Hence, mAbp1 is likely to constitute a downstream effector of Fyb involved in F-actin dynamics.     

Soluble expression, purification, and stabilization of a pro-apoptotic human protein, CARP

CARP is a novel pro-apoptotic protein that has been cloned and characterized in our previous report. Previous studies showed that suppression of CARP expression results in cell proliferation in several mammalian cell lines and over-expression of CARP leads to apoptosis and inhibition of proliferation in seven tumor cell lines [Liu et al., CARP is a novel caspase recruitment domain containing pro-apoptotic protein, Biochem. Biophys. Res. Commun. 293 (2002) 1396]. To obtain soluble and active form of CARP protein for further functional and structural studies, we have expressed CARP in Escherichia coli by using Gateway cloning system. Optimal induction and expression conditions were also studied. Recombinant histidine-tagged CARP was expressed in E. coli when the carp gene was subcloned into a Gateway expression vector pET21-DEST. The partially soluble recombinant CARP protein was purified to near homogeneity by a two-step FPLC procedure, first by Ni2+ affinity chromatography followed by a gel-filtration chromatography, which yielded about 10 mg protein/L culture with at least 95% purity. Two peaks were detected in the analytical gel-filtration chromatograph while only one peak corresponding to monomer of the CARP protein was left after adding 2 mM dithiothreitol (DTT). The polymers observed are likely due to the formation of intermolecular disulfide bridges. These results suggest that adding DTT is a good solution to prevent the formation of disulfide bonds and to stabilize the protein. Successfully growing crystals of the purified CARP protein also proved that we can produce well folded CARP protein in E. coli.     

A mitochondrial chaperonin: genetic, biochemical, and molecular characteristics

Mitochondria contain a matrix-localized protein complex composed of subunits homologous to the E.coli protein groEL. As with groEL in E.coli, the nuclear gene coding for the mitochondrial protein is essential for cell survival and the accumulation of the protein is elevated at heat shock-inducing temperatures. Biochemical analyses of wild type and mutant yeast strains have shown that this protein, hsp60, is required for the correct folding and assembly of newly imported, mitochondrially-targeted proteins. There is evidence suggesting a mandatory interaction between hsp60 and many imported, as well as mitochondrially-synthesized, proteins. The implications of these and other data are discussed.     

Molecular cloning, expression, and characterization of myo-inositol oxygenase from mouse, rat, and human kidney

myo-Inositol oxygenase (MIOX) is a non-heme iron enzyme, which catalyzes the conversion of myo-inositol to d-glucuronic acid, the first committed step in myo-inositol catabolism. Full-length cDNAs of 858bp each coding for 33kDa protein were cloned from kidney cDNA libraries of mouse, rat, and human. The individual clones were expressed in Escherichia coli and recombinant MIOX proteins were purified to electrophoretic homogeneity. A hydrophobic interaction chromatography step yielded multiple conformers, with mouse and human MIOX showing three peaks and rat enzyme revealing two peaks. Individual MIOX peaks exhibited distinct V(max) and K(m) values. Interestingly, upon storage, the 33kDa protein was degraded to a approximately 30kDa truncated protein in each species, and formed small amounts of dimers of identical subunits. While MIOX is a highly conserved enzyme in all mammalian species, the labile nature and tendency to degrade in solution may be the source of significant differences in size previously reported in the literature. Regardless of the source, our results strongly dispel previous conflicting literature reports on the size of the protein and confirm that MIOX is a 33kDa protein.     

Matrilysin: Expression, purification, and characterization

The expression vector pGEX-2T under the control of the IPTG-inducibletac promotor is effective for the production of a fusion protein of glutathione transferase (GST, 26 kDa) and promatrilysin (28 kDa) separated from the C-terminus of GST by a thrombin cleavage site. Zwittergen (palmityl sulfobetaine), 2%, solubilizes the fusion protein that is found associated with inclusion bodies. The solubilized fusion protein is purified by affinity chromatography on GSH agarose. Promatrilysin is obtained by thrombin cleavage either on the column or after GSH elution of the fusion protein. Mono S chromatography of the recovered protein yields homogeneous promatrilysin. The zinc content of promatrilysin and its activated enzyme product is slightly greater than 2 mol of zinc per mole of protein. The results indicate that the matrix metalloproteinases (MMPs) contain two metal-binding sites at which zinc is firmly bound and possibly a third site at which it is weakly bound. Primary sequence alignments for all the MMPs have a sequence homologous to the zinc-binding site of astacin,HExxHxxGxxH, suggesting one of the zinc sites is a catalytic one, in agreement with the known inhibition of these enzymes by chelators. However, the other zinc-binding site(s) likely reflect the different ways that astacin and the MMP subfamilies are stabilized, i.e., disulfides in astacin and metal ions in the MMPs.     

G-rich, a Drosophila selenoprotein, is a Golgi-resident type III membrane protein

G-rich is a Drosophila melanogaster selenoprotein, which is a homologue of human and mouse SelK. Subcellular localization analysis using GFP-tagged G-rich showed that G-rich was localized in the Golgi apparatus. The fusion protein was co-localized with the Golgi marker proteins but not with an endoplasmic reticulum (ER) marker protein in Drosophila SL2 cells. Bioinformatic analysis of G-rich suggests that this protein is either type II or type III transmembrane protein. To determine the type of transmembrane protein experimentally, GFP-G-rich in which GFP was tagged at the N-terminus of G-rich, or G-rich-GFP in which GFP was tagged at the C-terminus of G-rich, were expressed in SL2 cells. The tagged proteins were then digested with trypsin, and analyzed by Western blot analysis. The results showed that the C-terminus of the G-rich protein was exposed to the cytoplasm indicating it is a type III microsomal membrane protein. G-rich is the first selenoprotein identified in the Golgi apparatus.     

Overexpression, purification, sequence analysis, and characterization of the T4 bacteriophage dda DNA helicase.

The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. Oligonucleotide probes based on NH2-terminal amino acid sequence were used to precisely map the location of the dda gene on the T4 chromosome. Using polymerase chain reaction techniques, the dda gene was then cloned into an expression vector, and the overproduced protein was purified in two chromatography steps. Both the genomic and cloned dda genes were sequenced and found to be identical, encoding a protein of 439 amino acids. The dda protein contains amino acid sequences resembling those of other known helicases, and is most homologous to the Escherichia coli recD protein. Protein affinity chromatography was used to show a direct interaction between the dda protein and the T4 uvsX protein (a rec A-type DNA recombinase).     

Back Cover Image,Volume 117, Number 2, February 2020

During the manufacturing process, solutions of protein-based drugs are exposed to hydrodynamic forces, which can potentially affect protein stability and aggregation. Despite being an area of extensive investigation, the effect of hydrodynamic flow on protein aggregation is still controversial. In this study, we designed an experimental setup that allowed us to investigate flow- and interface-induced protein aggregation of two model immunoglobulins in the presence of well-defined flow stresses and solid–liquid interfaces. Within the range of shear rates typically encountered in bioprocessing (), we observed that increasing the shear rate by three orders of magnitude had a negligible effect on protein aggregation. By contrast, changes in the materials of the syringe barrels had a dramatic effect on the monomer loss, demonstrating the key role of solid–liquid interfaces in flow-induced aggregation. This finding was confirmed by the observed inverse dependence of the aggregation rate on the initial protein concentration, which is inconsistent with mechanisms of protein aggregation in bulk solution. Overall, our results reveal the presence of a synergistic effect of interfaces and hydrodynamic flow in flow-induced protein aggregation, which arises from the formation of protein particles or films on interfaces followed by displacement by flow or mechanical scraping.     

DANCE, a novel secreted RGD protein expressed in developing, atherosclerotic, and balloon-injured arteries.

We have identified and characterized mouse, rat, and human cDNAs that encode a novel secreted protein of 448 amino acids named DANCE (developmental arteries and neural crest epidermal growth factor (EGF)-like). DANCE contains six calcium-binding EGF-like domains, one of which includes an RGD motif. Overexpression studies of recombinant DANCE protein document that DANCE is a secreted 66-kDa protein. DANCE and recently described protein S1-5 comprise a new EGF-like protein family. The human DANCE gene was mapped at chromosome 14q32.1. DANCE mRNA is mainly expressed in heart, ovary, and colon in adult human tissues. Expression profile analysis by in situ hybridization revealed prominent DANCE expression in developing arteries. DANCE is also expressed in neural crest cell derivatives, endocardial cushion tissue, and several other mesenchymal tissues. In adult vessels, DANCE expression is largely diminished but is reinduced in balloon-injured vessels and atherosclerotic lesions, notably in intimal vascular smooth muscle cells and endothelial cells that lose their ability to proliferate in late stage of injury. DANCE protein was shown to promote adhesion of endothelial cells through interaction of integrins and the RGD motif of DANCE. DANCE is thus a novel vascular ligand for integrin receptors and may play a role in vascular development and remodeling.