A decade and a half of protein intrinsic disorder: Biology still waits for physics

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.     

Examining post‐translational modification‐mediated protein–protein interactions using a chemical proteomics approach

Post‐translational modifications (PTM) of proteins can control complex and dynamic cellular processes via regulating interactions between key proteins. To understand these regulatory mechanisms, it is critical that we can profile the PTM‐dependent protein–protein interactions. However, identifying these interactions can be very difficult using available approaches, as PTMs can be dynamic and often mediate relatively weak protein–protein interactions. We have recently developed CLASPI (cross‐linking‐assisted and stable isotope labeling in cell culture‐based protein identification), a chemical proteomics approach to examine protein–protein interactions mediated by methylation in human cell lysates. Here, we report three extensions of the CLASPI approach. First, we show that CLASPI can be used to analyze methylation‐dependent protein–protein interactions in lysates of fission yeast, a genetically tractable model organism. For these studies, we examined trimethylated histone H3 lysine‐9 (H3K9Me₃)‐dependent protein–protein interactions. Second, we demonstrate that CLASPI can be used to examine phosphorylation‐dependent protein–protein interactions. In particular, we profile proteins recognizing phosphorylated histone H3 threonine‐3 (H3T3‐Phos), a mitotic histone “mark” appearing exclusively during cell division. Our approach identified survivin, the only known H3T3‐Phos‐binding protein, as well as other proteins, such as MCAK and KIF2A, that are likely to be involved in weak but selective interactions with this histone phosphorylation “mark”. Finally, we demonstrate that the CLASPI approach can be used to study the interplay between histone H3T3‐Phos and trimethylation on the adjacent residue lysine 4 (H3K4Me₃). Together, our findings indicate the CLASPI approach can be broadly applied to profile protein–protein interactions mediated by PTMs.     

Genome-wide analysis of Nilaparvata lugens nymphal responses to high-density and low-quality rice hosts

The brown planthopper （BPH） Nilaparvata lugens is an economically impor- tant pest on rice plants. In this study, the higher population density and yellow-ripe stage of rice plants were used to construct adverse survival conditions （ASC） against BPH nymphs. Simultaneously, the low population density and tillering stage of rice plants were used to establish a suitable survival condition （SSC） as a control. Solexa/Illumina sequencing was used to identify genes of BPH nymphs responding to ASC. Significantly longer duration development of BPH nymphs and significantly lower brachypterous ratio of BPH adults were observed by ASC compared with SSC. A total of 2 544 differentially expressed genes （DEGs） were obtained and analyzed by BLASTx, Gene Ontology and KEGG Orthology. Gene ontology analysis revealed that the DEGs were mainly involved in categories of cell, cell part, cellular process, binding, catalytic, organelle and metabolic processes. 1138 DEGs having enzyme commission numbers were assigned to different metabolic pathways. The largest clusters were neurodegenerative diseases （137, 12.0%）, followed by carbohy- drate metabolism （113, 9.9%）, amino acid metabolism （94, 8.3%）, nucleotide metabolism （76, 6.7%）, energy metabolism （64, 5.6%）, translation （60, 5.3%）, lipid metabolism （58, 5.1%）, and folding, sorting and degradation （52, 4.6%）. Expressing profile of 11 DEGs during eight nymphal developmental stages of BPH were analyzed by quantitative real- time polymerase chain reaction. The 11 genes exhibited differential expression between ASC and SSC during at least one developmental stage. The DEGs identified in this study provide molecular proof of how BPH reconfigures its gene expression profile to adapt to overcrowding and low-quality hosts.     

The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution

Strong selection on parasites, as well as on hosts, is crucial for fueling coevolutionary dynamics. Selection will be especially strong if parasites that encounter resistant hosts are destroyed and diluted from the local environment. We tested whether spores of the bacterial parasite Pasteuria ramosa were passed through the gut (the route of infection) of their host, Daphnia magna, and whether passaged spores remained viable for a “second chance” at infecting a new host. In particular, we tested if this viability (estimated via infectivity) depended on host genotype, whether or not the genotype was susceptible, and on initial parasite dose. Our results show that Pasteuria spores generally remain viable after passage through both susceptible and resistant Daphnia. Furthermore, these spores remained infectious even after being frozen for several weeks. If parasites can get a second chance at infecting hosts in the wild, selection for infection success in the first instance will be reduced. This could also weaken reciprocal selection on hosts and slow the coevolutionary process.     

Matrix effects during monitoring of antibody and host cell proteins using attenuated total reflection spectroscopy

Production of recombinant proteins, e.g. antibodies, requires constant real‐time monitoring to optimize yield and quality attributes and to respond to changing production conditions, such as host cell protein (HCP) titers. To date, this monitoring of mammalian cell culture‐based processes is done using laborious and time consuming enzyme‐linked immunosorbent assays (ELISA), two‐dimensional sodium dodecylsulphate polyacrylamide gel electrophoresis, and chromatography‐based systems. Measurements are usually performed off‐line, requiring regular sample withdrawal associated with increased contamination risk. As information is obtained retrospectively, the reaction time to adapt to process changes is too long, leading to lower yield and higher costs. To address the resulting demand for continuous online‐monitoring systems, we present a feasibility study using attenuated total reflection spectroscopy (ATR) to monitor mAb and HCP levels of NS0 cell culture in situ, taking matrix effects into account. Fifty‐six NS0 cell culture samples were treated with polyelectrolytes for semi‐selective protein precipitation. Additionally, part of the samples was subjected to filtration prior to analysis, to change the background matrix and evaluate effects on chemometric quantification models. General models to quantify HCP and mAb in both filtered and unfiltered matrix showed lower prediction accuracy compared to models designed for a specific matrix. HCP quantification in the range of 2,000–55,000 ng mL^?1 using specific models was accurate for most samples, with results within the accepted limit of an ELISA assay. In contrast, mAb prediction was less accurate, predicting mAb in the range of 0.2–1.7 g L^?1. As some samples deviated substantially from reference values, further investigations elucidating the suitability of ATR for monitoring are required. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

Photosynthetic responses and acclimation of two castor bean cultivars to repeated drying–wetting cycles

To investigate the responses of castor bean to repeated drying–wetting cycles (RDWC), morpho-physiological parameters of two cultivars (Jiaxiang 2 and Hangbi 8) were determined by a pot experiment under well-watered control and RDWC. RDWC inhibited plant growth and leaf development, decreased water loss rate (WLR), and enhanced leaf mass per area (LMA) and chlorophyll content as indicated by spectral reflectance indices for both cultivars. Photosynthesis was inhibited by progressive drought stress but quickly recovered after rewatering for each cycle. Both cultivars exhibit a similar pattern of acclimation to RDWC: (1) higher LMA and lower WLR, (2) increased photosynthetic capacity under drought stress with increasing cycle numbers, (3) quick recovery and over-compensation for photosynthesis after rewatering, and (4) increased chlorophyll content. Jiaxiang 2 shows a high capacity for water preservation under drought stress and an over-compensation for photosynthesis after rewatering compared with Hangbi 8.     

Instability in a generalized Keller–Segel model

We present a generalized Keller–Segel model where an arbitrary number of chemical compounds react, some of which are produced by a species, and one of which is a chemoattractant for the species. To investigate the stability of homogeneous stationary states of this generalized model, we consider the eigenvalues of a linearized system. We are able to reduce this infinite dimensional eigenproblem to a parametrized finite dimensional eigenproblem. By matrix theoretic tools, we then provide easily verifiable sufficient conditions for destabilizing the homogeneous stationary states. In particular, one of the sufficient conditions is that the chemotactic feedback is sufficiently strong. Although this mechanism was already known to exist in the original Keller–Segel model, here we show that it is more generally applicable by significantly enlarging the class of models exhibiting this instability phenomenon which may lead to pattern formation.     

In situ ruminal degradation of amino acids and in vitro protein digestibility of undegraded CP of dried distillers’ grains with solubles from European ethanol plants

The objectives of this study were to compare the in situ ruminal degradation of CP and amino acids (AAs) of dried distillers’ grains with solubles (DDGS), and to estimate intestinal digestibility (ID) of undegradable crude protein (UDP) with the in vitro pepsin–pancreatin solubility of CP (PPS), using either DDGS samples (DDGS-s) or DDGS residues (DDGS-r) obtained after 16 h ruminal incubation. Thirteen samples originating from wheat, corn, barley and blends were studied. Lysine and methionine content of DDGS-s varied from 1.4 to 4.0 and 1.3 to 2.0 g/16 g N, respectively. The milk protein score (MPS) of DDGS-s was low and ranged from 0.36 to 0.51, and lysine and isoleucine were estimated to be the most limiting AAs in DDGS-s and DDGS-r. DDGS-r contained slightly more essential AAs (EAAs) than did the DDGS-s. Rumen degradation after 16 h varied from 44% to 94% for CP, from 39% to 90% for lysine and from 35% to 92% for methionine. Linear regressions showed that the ruminal degradation of individual AAs can be predicted from CP degradation. The PPS of DDGS-s was higher than that of DDGS-r and it varied from 70% to 89% and from 47% to 81%, respectively. There was no significant correlation between the PPS of DDGS-s and PPS of DDGS-r (R²=0.31). The estimated intestinally absorbable dietary protein (IADP) averaged 21%. Moderate correlation was found between the crude fibre (CF) content and PPS of DDGS-r (R²=0.43). This study suggests an overestimation of the contribution of UDP of DDGS to digestible protein supply in the duodenum in some currently used protein evaluation systems. More research is required and recommended to assess the intestinal digestibility of AAs from DDGS.     

Suitability of cross-bred cows for organic farms based on cross-breeding effects on production and functional traits

Data from 113 Dutch organic farms were analysed to determine the effect of cross-breeding on production and functional traits. In total, data on 33 788 lactations between January 2003 and February 2009 from 15 015 cows were available. Holstein–Friesian pure-bred cows produced most kg of milk in 305 days, but with the lowest percentages of fat and protein of all pure-bred cows in the data set. Cross-breeding Holstein dairy cows with other breeds (Brown Swiss, Dutch Friesian, Groningen White Headed, Jersey, Meuse Rhine Yssel, Montbéliarde or Fleckvieh) decreased milk production, but improved fertility and udder health in most cross-bred animals. In most breeds, heterosis had a significant effect (P < 0.05) on milk (kg in 305 days), fat and protein-corrected milk production (kg in 305 days) and calving interval (CI) in the favourable direction (i.e. more milk, shorter CI), but unfavourably for somatic cell count (higher cell count). Recombination was unfavourable for the milk production traits, but favourable for the functional traits (fertility and udder health). Farm characteristics, like soil type or housing system, affected the regression coefficients on breed components significantly. The effect of the Holstein breed on milk yield was twice as large in cubicle housing as in other housing systems. Jerseys had a negative effect on fertility only on farms on sandy soils. Hence, breed effects differ across farming systems in the organic farming and farmers can use such information to dovetail their farming system with the type of cow they use.