A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli

MOTIVATION: Inclusion body formation has been a major deterrent for overexpression studies since a large number of proteins form insoluble inclusion bodies when overexpressed in Escherichia coli. The formation of inclusion bodies is known to be an outcome of improper protein folding; thus the composition and arrangement of amino acids in the proteins would be a major influencing factor in deciding its aggregation propensity. There is a significant need for a prediction algorithm that would enable the rational identification of both mutants and also the ideal protein candidates for mutations that would confer higher solubility-on-overexpression instead of the presently used trial-and-error procedures. RESULTS: Six physicochemical properties together with residue and dipeptide-compositions have been used to develop a support vector machine-based classifier to predict the overexpression status in E.coli. The prediction accuracy is approximately 72% suggesting that it performs reasonably well in predicting the propensity of a protein to be soluble or to form inclusion bodies. The algorithm could also correctly predict the change in solubility for most of the point mutations reported in literature. This algorithm can be a useful tool in screening protein libraries to identify soluble variants of proteins.     

Effects of salt on the thermal stability of human plasma high-density lipoprotein

High-density lipoproteins (HDL) mediate cholesterol removal and thereby protect against atherosclerosis. Mature spherical HDL contain the apolar lipid core and polar surface of proteins and phospholipids. Earlier, we showed that the structural integrity of HDL is modulated by kinetic barriers that prevent spontaneous protein dissociation and lipoprotein fusion and rupture. To determine the role of electrostatic interactions in the kinetic stability of mature HDL, here we analyze the effects of salt and pH on their thermal denaturation. In low-salt buffer at pH 5.7-7.7, HDL are highly thermostable. Increasing the salt concentration from 0 to 0.3 M NaCl causes low-temperature shifts in the calorimetric HDL transitions of up to -14 degrees C. This salt-induced destabilization leads to protein unfolding below 100 degrees C, facilitating the first Arrhenius analysis of HDL denaturation by circular dichroism spectroscopy. In 150 mM NaCl, two kinetic phases in HDL protein unfolding are observed: a faster phase with an activation energy E(a,fast) < or =15 kcal/mol and a slower phase with an E(a,slow) = 50 +/- 7 kcal/mol. Gel electrophoresis and electron microscopic data suggest that the faster phase involves partial protein unfolding but no significant protein dissociation or changes in HDL size, while the slower phase involves complete protein unfolding, partial protein dissociation, and HDL fusion. Hence, the slower phase may resemble HDL remodeling and fusion by plasma enzymes during metabolism. Analysis of the effects of various salts, sucrose, and pH suggests that HDL destabilization by salt results from ionic screening of favorable short-range electrostatic interactions such as salt bridges. Consequently, electrostatic interactions significantly contribute to the high thermostability of HDL in low-salt solutions.     

Uniform binding and negative catalysis at the origin of enzymes

Enzymes are well known for their catalytic abilities, some even reaching “catalytic perfection” in the sense that the reaction they catalyze has reached the physical bound of the diffusion rate. However, our growing understanding of enzyme superfamilies has revealed that only some share a catalytic chemistry while others share a substrate‐handle binding motif, for example, for a particular phosphate group. This suggests that some families emerged through a “substrate‐handle‐binding‐first” mechanism (“binding‐first” for brevity) instead of “chemistry‐first” and we are, therefore, left to wonder what the role of non‐catalytic binders might have been during enzyme evolution. In the last of their eight seminal, back‐to‐back articles from 1976, John Albery and Jeremy Knowles addressed the question of enzyme evolution by arguing that the simplest mode of enzyme evolution is what they defined as “uniform binding” (parallel stabilization of all enzyme‐bound states to the same degree). Indeed, we show that a uniform‐binding proto‐catalyst can accelerate a reaction, but only when catalysis is already present, that is, when the transition state is already stabilized to some degree. Thus, we sought an alternative explanation for the cases where substrate‐handle‐binding preceded any involvement of a catalyst. We find that evolutionary starting points that exhibit negative catalysis can redirect the reaction''s course to a preferred product without need for rate acceleration or product release; that is, if they do not stabilize, or even destabilize, the transition state corresponding to an undesired product. Such a mechanism might explain the emergence of “binding‐first” enzyme families like the aldolase superfamily.     

The distribution pattern of alpha-MSH-like immunoreactivity in the cat central nervous system

The distribution pattern of alpha-melanocyte stimulating hormone-like immunoreactivity (alpha-MSH-Li) was studied in cats using avidin-biotin modification of immunocytochemical method. Cell bodies containing alpha-MSH-Li were observed in the medial basal hypothalamus, especially in the infundibular nucleus, the lateral hypothalamus and near zona incerta. Fibers with alpha-MSH-Li extended beyond the hypothalamus, into the paraventricular nucleus of the thalamus, rostral amygdala, periaqueductal gray, locus ceruleus, parabrachial nucleus and medial nucleus of the nucleus tractus solitarius. Axons with alpha-MSH-Li were also seen diffusely in various cortical areas, but more extensively in the limbic cortical regions. The distribution pattern of the cell bodies and fibers containing alpha-MSH-Li bears several similarities to that seen in rats, but differs in that the alpha-MSH-Li was not observed in cell bodies in locations other than the medial basal and lateral hypothalamus.     

Electron density profile of two-dimensionally crystalline membranous cytochrome c oxidase at low resolution.

Unilamellar vesicles of membranous cytochrome c oxidase have been isolated whose distribution of protein in the membrane plane was predominantly crystalline. The vesicles were collapsed via controlled partial dehydration, resulting, at first, in the formation of unoriented, mostly unstacked, membrane pairs. Further controlled partial dehydration resulted in the formation of oriented multilayers of stacks of membrane pairs, retaining the in-plane crystallinity. The above were monitored by electron microscopy and x-ray diffraction. Analysis of the x-ray diffraction from unoriented, unstacked membrane pairs by two independent methods provided the membrane electron density profile to 30 A resolution.     

The use of nonspecific T acceptor cells to overcome the aberrant function of antigen-specific third-order T suppressor cells

Earlier studies in the phenyltrimethylamino (TMA) hapten system demonstrated that under certain conditions idiotype-specific second-order T suppressor (Ts2)-bearing mice fail to suppress TMA-specific delayed-type hypersensitivity. This was due to a functional deletion in the third-order T suppressor (Ts3) subset. In this report we have confirmed and extended these findings to show that only homologous TMA-specific Ts3 can restore suppressor function, both heterologous Ts3 and unprimed T-cell populations failed to do so. Furthermore, attempts to induce Ts3 function in the defective mice after reconstitution with normal precursor Ts3 cells also failed. In contrast, protocols which induce heterologous contact and cutaneous hypersensitivity reactions readily induced cell populations capable of restoring suppression in the Ts3-defective mice. Analysis of the lymphoid populations from the contact-sensitized defective mice revealed that these cells were not the prototypical Ts3 but were similar to the previously reported nonspecific T acceptor cell. The results further indicated that the T acceptor cell functioned as the active terminal-phase Ts subset, and this could be used as an alternative to the TMA-specific Ts3. The importance of multiple suppressor pathways at the terminal phase of immune suppression is discussed.     

Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification

Background

Non-productive binding of enzymes to lignin is thought to impede the saccharification efficiency of pretreated lignocellulosic biomass to fermentable sugars. Due to a lack of suitable analytical techniques that track binding of individual enzymes within complex protein mixtures and the difficulty in distinguishing the contribution of productive (binding to specific glycans) versus non-productive (binding to lignin) binding of cellulases to lignocellulose, there is currently a poor understanding of individual enzyme adsorption to lignin during the time course of pretreated biomass saccharification.

Results

In this study, we have utilized an FPLC (fast protein liquid chromatography)-based methodology to quantify free Trichoderma reesei cellulases (namely CBH I, CBH II, and EG I) concentration within a complex hydrolyzate mixture during the varying time course of biomass saccharification. Three pretreated corn stover (CS) samples were included in this study: Ammonia Fiber Expansion^a (AFEX?-CS), dilute acid (DA-CS), and ionic liquid (IL-CS) pretreatments. The relative fraction of bound individual cellulases varied depending not only on the pretreated biomass type (and lignin abundance) but also on the type of cellulase. Acid pretreated biomass had the highest levels of non-recoverable cellulases, while ionic liquid pretreated biomass had the highest overall cellulase recovery. CBH II has the lowest thermal stability among the three T. reesei cellulases tested. By preparing recombinant family 1 carbohydrate binding module (CBM) fusion proteins, we have shown that family 1 CBMs are highly implicated in the non-productive binding of full-length T. reesei cellulases to lignin.

Conclusions

Our findings aid in further understanding the complex mechanisms of non-productive binding of cellulases to pretreated lignocellulosic biomass. Developing optimized pretreatment processes with reduced or modified lignin content to minimize non-productive enzyme binding or engineering pretreatment-specific, low-lignin binding cellulases will improve enzyme specific activity, facilitate enzyme recycling, and thereby permit production of cheaper biofuels.