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ATP synthase, a highly conserved protein complex that has a subunit composition of α3 β3 γδeab2 c8-15 for the bacterial enzyme, is a key player in supplying energy to living organisms. This protein complex consists of a peripheral F1 sector (α3 β3 γδe) and a membrane-integrated Fo sector (ab2 c8-15 ). Structural analyses of the isolated protein components revealed that, remarkably, the C-terminal domain of its e-subunit seems to adopt two dramatically different structures, but the physiological relevance of this conformational change remains largely unknown. In an attempt to decipher this, we developed a high-throughput in vivo protein photo-cross-linking analysis pipeline based on the introduction of the unnatural amino acid into the target protein via the scarless genome-targeted site-directed mutagenesis technique, and probing the cross-linked products via the high-throughput polyacrylamide gel electrophoresis technique. Employing this pipeline, we examined the interactions involving the C-terminal helix of the e-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the bacterial ATP synthase exists as an equilibrium between the 'inserted' and 'noninserted' state in cells, maintaining a moderate but significant level of net ATP synthesis when shifting to the former upon exposing to unfavorable energetically stressful conditions. Such a mechanism allows the bacterial ATP synthases to proportionally and instantly switch between two reversible functional states in responding to changing environmental conditions. Importantly, this high-throughput approach could allow us to decipher the physiological relevance of protein-protein interactions identified under in vitro conditions or to unveil novel physiological context-dependent protein-protein interactions that are unknown before.

Human diseases are usually linked to multiloci genetic alterations, including single‐nucleotide polymorphisms (SNPs). Methods to use these SNPs for disease risk prediction (DRP) are of clinical interest. DRP algorithms explored by commercial companies to date have tended to be complex and led to controversial prediction results. Here, we present a general approach for establishing a logistic model‐based DRP algorithm, in which multiple SNP risk factors from different publications are directly used. In particular, the coefficient β of each SNP is set as the natural logarithm of the reported odds ratio, and the constant coefficient β0 is comprehensively determined by the coefficient and frequency of each SNP and the average disease risk in populations. Furthermore, homozygous SNP is considered a dummy variable, and the SNPs are updated (addition, deletion and modification) if necessary. Importantly, we validated this algorithm as a proof of concept: two patients with lung cancer were identified as the maximum risk cases from 57 Chinese individuals. Our logistic model‐based DRP algorithm is apparently more intuitive and self‐evident than the algorithms explored by commercial companies, and it may facilitate DRP commercialization in the era of personalized medicine.

DegP (also designated as HtrA) and its homologs are found in prokaryotic cells and such eukaryotic organelles as mitochondria and chloroplasts. DegP has been found to be essential for the growth of Gram-negative bacteria under heat shock conditions and arguably considered to possess both protease and chaperone activities. The function of DegP has not been clearly defined. Using genetically incorporated non-natural amino acids as photo-crosslinkers, here we identified the β-barrel outer membrane proteins (OMPs) as the major natural substrates of DegP in Escherichia coli cells. We also demonstrated that DegP primarily functions as a protease, at both low and high temperatures, to eliminate unfolded OMPs, with hardly any appreciable chaperone activity in cells. We also found that the toxic and cell membrane-damaging misfolded OMPs would accumulate in DegP-lacking cells cultured under heat shock conditions. Together, our study defines the primary function of DegP in OMP biogenesis and offers a mechanistic insight into the essentiality of DegP for cell growth under heat shock conditions. Structured digital abstract DegP physically interacts with ompA by pull down (1, 2) DegP physically interacts with ompX, ompA, ompW, ompF, nmpC and ompC by pull down (View interaction) DegP physically interacts with ompC and ompF by pull down (View interaction) DegP physically interacts with ompC and ompA by pull down (View interaction) DegP physically interacts with ompC, malE, fkpA, ompW, ompA, ompF, nmpC and ompX by cross-linking study (View interaction)

Small heat shock proteins (sHSPs) are ubiquitous molecular chaperones that prevent the aggregation of various non-native proteins and play crucial roles for protein quality control in cells. It is poorly understood what natural substrate proteins, with respect to structural characteristics, are preferentially bound by sHSPs in cells. Here we compared the structural characteristics for the natural substrate proteins of Escherichia coli IbpB and Deinococcus radiodurans Hsp20.2 with the respective bacterial proteome at multiple levels, mainly by using bioinformatics analysis. Data indicate that both IbpB and Hsp20.2 preferentially bind to substrates of high molecular weight or moderate acidity. Surprisingly, their substrates contain abundant charged residues but not abundant hydrophobic residues, thus strongly indicating that ionic interactions other than hydrophobic interactions also play crucial roles for the substrate recognition and binding of sHSPs. Further, secondary structure prediction analysis indicates that the substrates of low percentage of β-sheets or coils but high percentage of α-helices are un-favored by both IbpB and Hsp20.2. In addition, IbpB preferentially interacts with multi-domain proteins but unfavorably with α + β proteins as revealed by SCOP analysis. Together, our data suggest that bacterial sHSPs, though having broad substrate spectrums, selectively bind to substrates of certain structural features. These structural characteristic elements may substantially participate in the sHSP-substrate interaction and/or increase the aggregation tendency of the substrates, thus making the substrates more preferentially bound by sHSPs.

As a class of molecular chaperones, small heat shock proteins (sHsps) usually exist as multi-subunit spherical oligomers. In this study, we report that AgsA, a sHsp of Salmonella enterica serovar Typhimurium, spontaneously forms fibrils in vitro. These fibrils tend to be formed at elevated temperature and do not share the characteristics of amyloid. Interestingly, the fibril-forming AgsA is able to suppress the dithiothreitol-induced aggregation of insulin efficiently within a certain range of temperature. During this process, AgsA fibrils disappear and spherical complexes form between AgsA and insulin molecules. These data suggest that AgsA fibrils may represent a distinctive type of structural and functional form of sHsp from spherical oligomers. Our study provides new insights into sHsp structures and chaperone functions.Structured summary of protein interactionsAgsA and AgsA bind by electron microscopy (View interaction).Insulin and Insulin bind by molecular sieving (View interaction).Insulin and Insulin bind by electron microscopy (View interaction).AgsA and AgsA bind by molecular sieving (View interaction).AgsA and AgsA bind by fluorescence technology (View interaction).AgsA and AgsA bind by circular dichroism (View interaction).Insulin and Insulin bind by fluorescence technology (View interaction).AgsA and Insulin bind by molecular sieving (View interaction).AgsA and AgsA bind by electron tomography (View interaction).

Many cellular proteins exist as homo-oligomers. The mechanism of the assembly process of such proteins is still poorly understood. We have previously observed that Hsp16.3, a protein exhibiting chaperone-like activity, undergoes stepwise disassembly and nonstepwise reassembly. Here, the disassembly and reassembly of a nonchaperone protein RbsD, from Escherichia coli, was studied in vitro. The protein was found to mainly exist as decamers with a small portion of apparently larger oligomeric forms, both of which are able to refold/reassemble effectively in a spontaneous way after being completely unfolded. Disassembly RbsD intermediates including pentamers, tetramers, trimers, dimers, and monomers were detected by using urea-containing pore gradient polyacrylamide gel electrophoresis, while only pentamers were detected for its reassembly. The observation of stepwise disassembly and apparent nonstepwise reassembly for both a chaperone protein (Hsp16.3) and a nonchaperone protein (RbsD) strongly suggests that such a feature is most likely general for homo-oligomeric proteins.