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Viruses of the order Nidovirales encode huge replicase polyproteins. These are processed primarily by the chymotrypsin-like main proteinases (M pro s). So far, M pro s have been studied only for corona-, arteri-, and roniviruses. Here, we report the characterization of the M pro of toroviruses, the fourth main Nidovirus branch. Comparative sequence analysis of polyprotein 1a of equine torovirus (EToV) strain Berne, identified a serine proteinase domain, flanked by hydrophobic regions. Heterologous expression of this domain resulted in autoprocessing at flanking cleavage sites. N-terminal sequence analysis of cleavage products tentatively identified FxxQ↓(S, A) as the substrate consensus sequence. EToV M pro combines several traits of its closest relatives. It has a predicted three-domain structure, with two catalyticβ -barrel domains and an additional C-terminal domain of unknown function. With respect to substrate specificity, the EToV M pro resembles its coronavirus homologue in its preference for P1-Gln, but its substrate-binding subsite, S1, more closely resembles that of arteri- and ronivirus M pro s, which prefer P1-Glu. Surprisingly, in contrast to the M pro s of corona- and roniviruses, but like that of arterivirus, the torovirus M pro uses serine instead of cysteine as its principal nucleophile. Under the premise that the M pro s of corona- and toroviruses are more closely related to each other than to those of arteri- and roniviruses, the transition from serine- to cysteine-based proteolytic catalysis (or vice versa) must have happened more than once in the course of nidovirus evolution. In this respect, it is of interest that a mutant EToV M pro with a Ser 165 →Cys substitution retained partial enzymatic activity.

Central to the transcriptional control of the Escherichia coli heat shock regulon is the stress-dependent inhibition of the s32 subunit of RNA polymerase by reversible association with the DnaK chaperone, mediated by the DnaJ cochaperone. Here we identified two distinct sites in s32 as binding sites for DnaK and DnaJ. DnaJ binding destabilizes a distant region of s32 in close spatial vicinity of the DnaK-binding site, and DnaK destabilizes a region in the N-terminal domain, the primary target for the FtsH protease, which degrades s32 in vivo. Our findings suggest a molecular mechanism for the DnaK- and DnaJmediated inactivation of s32 as part of the heat shock response. They furthermore demonstrate that DnaK and DnaJ binding can induce conformational changes in a native protein substrate even at distant sites, a feature that we propose to be of general relevance for the action of Hsp70 chaperone systems.

A correct three-dimensional structure is a prerequisite for protein functionality, and therefore for life. Thus, it is not surprising that our cells are packed with proteins that assist protein folding, the process in which the native three-dimensional structure is formed. In general, plasma membrane and secreted proteins, as well as those residing in compartments along the endocytic and exocytic pathways, fold and oligomerize in the endoplasmic reticulum. The proteins residing in the endoplasmic reticulum are specialized in the folding of this subset of proteins, which renders this compartment a protein-folding factory. This review focuses on protein folding in the endoplasmic reticulum, and discusses the challenge of oligomer formation in the endoplasmic reticulum as well as the cytosol.

Background: The HIV-1 envelope glycoprotein gp120, which mediates viral attachment to target cells, consists for ~50% of sugar, but the role of the individual sugar chains in various aspects of gp120 folding and function is poorly understood. Here we studied the role of the carbohydrate at position 386. We identified a virus variant that had lost the 386 glycan in an evolution study of a mutant virus lacking the disulfide bond at the base of the V4 domain. Results: The 386 carbohydrate was not essential for folding of wt gp120. However, its removal improved folding of a gp120 variant lacking the 385–418 disulfide bond, suggesting that it plays an auxiliary role in protein folding in the presence of this disulfide bond. The 386 carbohydrate was not critical for gp120 binding to dendritic cells (DC) and DC-mediated HIV-1 transmission to T cells. In accordance with previous reports, we found that N386 was involved in binding of the mannose-dependent neutralizing antibody 2G12. Interestingly, in the presence of specific substitutions elsewhere in gp120, removal of N386 did not result in abrogation of 2G12 binding, implying that the contribution of N386 is context dependent. Neutralization by soluble CD4 and the neutralizing CD4 binding site (CD4BS) antibody b12 was significantly enhanced in the absence of the 386 sugar, indicating that this glycan protects the CD4BS against antibodies. Conclusion: The carbohydrate at position 386 is not essential for protein folding and function, but is involved in the protection of the CD4BS from antibodies. Removal of this sugar in the context of trimeric Env immunogens may therefore improve the elicitation of neutralizing CD4BS antibodies.

ASPP2 is a pro-apoptotic protein that stimulates the p53-mediated apoptotic response. The C terminus of ASPP2 contains ankyrin (Ank) repeats and a SH3 domain, which mediate its interactions with numerous partner proteins such as p53,NF B, and Bcl-2. It also contains a proline-rich domain (ASPP2 Pro), whose structure and function are unclear. Here we used biophysical and biochemical methods to study the structure and the interactions of ASPP2 Pro, to gain insight into its biological role. We show, using biophysical and computational methods, that the ASPP2 Pro domain is natively unfolded. We found that the ASPP2 Pro domain interacts with the ASPP2 Ank-SH3 domains, and mapped the interaction sites in both domains. Using a combination of peptide array screening, biophysical and biochemical techniques, we found that ASPP2 Ank-SH3, but not ASPP2 Pro, mediates interactions of ASPP2 with peptides derived from its partner proteins. ASPP2 Pro-Ank-SH3 bound a peptide derived from its partner protein NF B weaker than ASPP2 Ank-SH3 bound this peptide. This suggested that the presence of the proline-rich domain inhibited the interactions mediated by the Ank-SH3 domains. Furthermore, a peptide from ASPP2 Pro competed with a peptide derived from NF B on binding to ASPP2 Ank-SH3. Based on our results, we propose a model in which the interaction between theASPP2domains regulates the intermolecular interactions of ASPP2 with its partner proteins.

Peroxisomesare one ofnumerous organelles in a eukaryotic cell; they are small, single-membrane-bound vesicles involved in cellular metabolism, particularly fatty acid degradation. Transport of metabolites and co-factors in and across the membrane is taken care of by specific transporters. Peroxisome formation and maintenance has been debated for a long time: opinions swinging from autonomous to ER-derived organelles. Only recently it has been established firmly that the site of origin of peroxisomes is the ER. It implies that a new branch of the endomembrane system is open to further characterization.

We have characterized the molecular basis of the interaction between ASPP2 and Bcl-2, which are key proteins in the apoptotic pathway. The C-terminal ankyrin repeats and SH3 domain of ASPP2 (ASPP2Ank-SH3) mediate its interactions with the antiapoptotic protein Bcl-2. We used biophysical and computational methods to identify the interaction sites of Bcl-2 and its homologues with ASPP2. Using peptide array screening, we found that ASPP2Ank-SH3 binds two homologous sites in all three Bcl proteins tested: (i) the conserved BH4 motif, and (ii) a binding site for proapoptotic regulators. Quantitative binding studies revealed that binding of ASPP2Ank-SH3 to the Bcl-2 family members is selective at two levels: (i) interaction with Bcl-2-derived peptides is the tightest compared to peptides from the other family members, and (ii) within Bcl-2, binding of ASPP2Ank-SH3 to the BH4 domain is tightest. Sequence alignment of the ASPP2-binding peptides combined with binding studies of mutated peptides revealed that two nonconserved positions where only Bcl-2 contains positively charged residues account for its tighter binding. The experimental binding results served as a basis for docking analysis, by which we modeled the complexes of ASPP2Ank-SH3 with the full-length Bcl proteins. Using peptide arrays and quantitative binding studies, we found that Bcl-2 binds three loops in ASPP2Ank-SH3 with similar affinity, in agreement with our predicted model. Based on our results, we propose a mechanism in which ASPP2 induces apoptosis by inhibiting functional sites of the antiapoptotic Bcl-2 proteins.

In eukaryotic cells, most newly synthesized secretory proteins are first translocated into the endoplasmic reticulum (ER) and transit through organelles that constitute a secretory pathway. However, a fraction of them never reach the desired native state. Instead, these proteins misfold in the ER and are retrotranslocated out of this organelle to the cytoplasm, where they are degraded by the ubiquitin- proteasome system (a process called ERassociated degradation). For efficient retrotranslocation, the disulfide bonds of misfolded proteins must be reduced, and on page 569 in this issue, Ushioda et al. (1) report that this reaction is catalyzed by ERdj5, the first dedicated reductase identified in the ER. The most abundant ER oxidoreductase, protein disulfide isomerase (PDI), contains two thioredoxin-like domains Cys-X-X-Cys (CXXC, where X is another, but not any, amino acid), and can make (oxidize), break (reduce), and isomerize disulfide bonds, depending on reaction conditions (2). In principle, PDI can do the reductase job as well as ERdj5 (3).

Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein’s folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins.

The amount of folded functional protein in a cell is controlled by a number of factors, including the relative rates of its biosynthetic and specific degradation processes, and its intrinsic thermodynamic stability. Mutationinduced loss of stability is a common cause of disease. Many oncogenic mutants of the tumour suppressor p53, for example, reduce the intrinsic thermodynamic stability of the protein in vitro. We have analysed the level of recombinant folded human p53 core domain (p53C) and its mutants in Escherichia coli spanning a stability range of 6 kcal/mol to assess the effects of intrinsic thermodynamic stability in vivo in the absence of specific ubiquitin-mediated pathways in human cells. The levels of folded protein were measured fluorimetrically in living cells by fusing the gene of p53C upstream to that of green fluorescent protein and measuring the fluorescence relative to a control at various temperatures. At a fixed temperature, the amount of fluorescence is correlated with the thermodynamic stability of the mutant. The level of each protein varied with temperature according to a sigmoid curve that paralleled the melting in vitro, but the apparent Tm was lower in vivo, because steady-state levels are observed rather than true thermodynamic equilibria. Our results show clearly that changes in the intrinsic thermodynamic stability of p53 reduce the level of folded and hence functional p53 substantially in E. coli, and provide insights into the correlation between protein instability and disease at the cellular level.

The majority of eukaryotic secretory and membrane proteins contain disulfide bonds, which are strongly conserved within protein families because of their crucial role in folding or function. The exact role of these disulfide bonds during folding is unclear. Using virus-driven evolution we generated a viral glycoprotein variant, which is functional despite the lack of an absolutely conserved disulfide bond that links two antiparallel beta-strands in a six-stranded beta-barrel. Molecular dynamics simulations revealed that improved hydrogen bonding and side chain packing led to stabilization of the beta-barrel fold, implying that beta-sheet preference codirects glycoprotein folding in vivo. Our results show that the interactions between two beta-strands that are important for the formation and/or integrity of the beta-barrel can be supported by either a disulfide bond or beta-sheet favoring residues.

We have characterized the molecular basis of the interaction between ASPP2 and Bcl-2, which are key proteins in the apoptotic pathway. The C-terminal ankyrin repeats and SH3 domain of ASPP2 (ASPP2 Ank-SH3 ) mediate its interactions with the antiapoptotic protein Bcl-2. We used biophysical and computational methods to identify the interaction sites of Bcl-2 and its homologues with ASPP2. Using peptide array screening, we found that ASPP2 Ank-SH3 binds two homologous sites in all three Bcl proteins tested: ( i ) the conserved BH4 motif, and ( ii ) a binding site for proapoptotic regulators. Quantitative binding studies revealed that binding of ASPP2 Ank-SH3 to the Bcl-2 family members is selective at two levels: ( i ) interaction with Bcl-2-derived peptides is the tightest compared to peptides from the other family members, and ( ii ) within Bcl-2, binding of ASPP2 Ank-SH3 to the BH4 domain is tightest. Sequence alignment of the ASPP2-binding peptides combined with binding studies of mutated peptides revealed that two nonconserved positions where only Bcl-2 contains positively charged residues account for its tighter binding. The experimental binding results served as a basis for docking analysis, by which we modeled the complexes of ASPP2 Ank-SH3 with the full-length Bcl proteins. Using peptide arrays and quantitative binding studies, we found that Bcl-2 binds three loops in ASPP2 Ank-SH3 with similar affinity, in agreement with our predicted model. Based on our results, we propose a mechanism in which ASPP2 induces apoptosis by inhibiting functional sites of the antiapoptotic Bcl-2 proteins.

International audience; Central to the transcriptional control of the Escherichia coli heat shock regulon is the stress-dependent inhibition of the sigma(32) subunit of RNA polymerase by reversible association with the DnaK chaperone, mediated by the DnaJ cochaperone. Here we identified two distinct sites in sigma(32) as binding sites for DnaK and DnaJ. DnaJ binding destabilizes a distant region of sigma(32) in close spatial vicinity of the DnaK-binding site, and DnaK destabilizes a region in the N-terminal domain, the primary target for the FtsH protease, which degrades sigma(32) in vivo. Our findings suggest a molecular mechanism for the DnaK- and DnaJ-mediated inactivation of sigma(32) as part of the heat shock response. They furthermore demonstrate that DnaK and DnaJ binding can induce conformational changes in a native protein substrate even at distant sites, a feature that we propose to be of general relevance for the action of Hsp70 chaperone systems.

ASPP2 is a pro-apoptotic protein that stimulates the p53-mediated apoptotic response. The C terminus of ASPP2 contains ankyrin (Ank) repeats and a SH3 domain, which mediate its interactions with numerous partner proteins such as p53, NFkappaB, and Bcl-2. It also contains a proline-rich domain (ASPP2 Pro), whose structure and function are unclear. Here we used biophysical and biochemical methods to study the structure and the interactions of ASPP2 Pro, to gain insight into its biological role. We show, using biophysical and computational methods, that the ASPP2 Pro domain is natively unfolded. We found that the ASPP2 Pro domain interacts with the ASPP2 Ank-SH3 domains, and mapped the interaction sites in both domains. Using a combination of peptide array screening, biophysical and biochemical techniques, we found that ASPP2 Ank-SH3, but not ASPP2 Pro, mediates interactions of ASPP2 with peptides derived from its partner proteins. ASPP2 Pro-Ank-SH3 bound a peptide derived from its partner protein NFkappaB weaker than ASPP2 Ank-SH3 bound this peptide. This suggested that the presence of the proline-rich domain inhibited the interactions mediated by the Ank-SH3 domains. Furthermore, a peptide from ASPP2 Pro competed with a peptide derived from NFkappaB on binding to ASPP2 Ank-SH3. Based on our results, we propose a model in which the interaction between the ASPP2 domains regulates the intermolecular interactions of ASPP2 with its partner proteins.

Hsp70 chaperones are involved in the prevention of misfolding, and possibly the folding, of newly synthesized proteins. The members of this chaperone family are capable of interacting with polypeptide chains both co- and posttranslationally, but it is currently not clear how different structural domains of the chaperone affect binding specificity. We explored the interactions between the bacterial Hsp70, DnaK, and the sequence of a model all-R-helical globin (apoMb) by cellulose-bound peptide scanning. The binding specificity of the full-length chaperone was compared with that of its minimal substrate-binding domain, DnaK-‚. Six specific chaperone binding sites evenly distributed along the apoMb sequence were identified. Binding site locations are identical for the full-length chaperone and its substrate- binding domain, but relative affinities differ. The binding specificity of DnaK- ‚ is only slightly decreased relative to that of full-length DnaK. DnaK's binding motif is known to comprise hydrophobic regions flanked by positively charged residues. We found that the simple fractional mean buried area correlates well with Hsp70's binding site locations along the apoMb sequence. In order to further characterize the properties of the minimal binding host, the stability of DnaK-‚ upon chemical denaturation by urea and protons was investigated. Urea unfolding titrations yielded an apparent folding ¢G° of 3.1 ( 0.9 kcal mol -1 and an m value of 1.7 ( 0.4 kcal mol -1 M -1 . ‡ Joint first authors. §