Volume change on formation of native collagen aggregate

The volume change which occurs in dilute tropocollagen solution as a result of the phase transition producing the “native” form of collagen aggregate has been measured dilatometrically. A volume increase of 0.8 × 10^?3 ml./g. collagen in phosphate buffer (pH 7–7.5) was determined. The volume expansion is attributed to a reduction in the organization of water molecules around nonpolar surfaces of the individual tropocollagen units. This volume expansion is consistent with a previous hypothesis that hydro-phobic bonding is the driving force in this collagen aggregation.     

Chaperone Effects on Prion and Nonprion Aggregates

Exposure to high temperature or other stresses induces a synthesis of heat shock proteins. Many of these proteins are molecular chaperones, and some of them help cells to cope with heat induced denaturation and aggregation of other proteins. In the last decade, chaperones have received increased attention in connection with their role in maintenance and propagation of the Saccharomyces cerevisiae prions, infectious or heritable agents transmitted at the protein level. Recent data suggest that functioning of the chaperones in reactivation of heat damaged proteins and in propagation of prions is based on the same molecular mechanisms but may lead to different consequences depending on the type of aggregate. In both cases the concerted and balanced action of “chaperones’ team”, including Hsp104, Hsp70, Hsp40 and possibly other proteins, determines whether a misfolded protein is to be incorporated into an aggregate, rescued to the native state or targeted for degradation.     

Conformational studies of alanine oligopeptides by nuclear magnetic resonance.

We have studied the nmr spectra of the series of alanine oligopeptides containing a methoxyethoxyethoxyacetyl blocking group on the N-terminal residue and a morpholino blocking group on the C-terminal residue. Spectra were measured in chloroform–trifluoroacetic acid solvent systems. For oligomers with chain lengths of five or more, “double peaks” are observed for the α-CH protons. Addition of trifluoroacetic acid causes the peaks to coalesce. The amount of trifluoroacetic acid necessary for coalescence increases from the pentamer to the nonamer. These findings are general since alanine oligomers with different blocking groups exhibit similar “double peak” phenomena. We explain the “double peak” phenomenon in terms of specific folded forms of the oligopeptides which arise from intramolecular hydrogen bonding. Additional evidence for such hydrogen bonding is presented based upon infrared studies. Slight aggregation probably occurs for the pentamer and hexamer which may stabilize the folded forms.     

DNA Facilitates Oligomerization and Prevents Aggregation via DNA Networks

Previous studies have shown that nucleic acids can nucleate protein aggregation in disease-related proteins, but in other cases, they can act as molecular chaperones that prevent protein aggregation, even under extreme conditions. In this study, we describe the link between these two behaviors through a combination of electron microscopy and aggregation kinetics. We find that two different proteins become soluble under harsh conditions through oligomerization with DNA. These DNA/protein oligomers form “networks,” which increase the speed of oligomerization. The cases of DNA both increasing and preventing protein aggregation are observed to stem from this enhanced oligomerization. This observation raises interesting questions about the role of nucleic acids in aggregate formation in disease states.     

The solution behavior of poly-L-proline: I. Light scattering studies in water and concentrated aqueous neutral salt solutions

The solution bebavior of poly-L -proline Form II has been studied in water and aqueous salt solutions by both elastic and quasi-elastic light -scattering techniques. The results of this study suggest that polyproline Form II can exist in water at 24 °C as an associated polymer complex and that certain salts which do not appear to affect the helix integrity, e.g., guanidinium-HCl, resutl in dissociation of the aggregate. Other neutral salts, of the variety effective in mediating unfolding of the Form II helix (e.g., 4M NaClO₄) also induce aggregate dissociation, but 4M CaCl₂ results in enhanced aggregation of polyproline. Kinetic experiments indicate that a time of 20 hours is necessary for the completion of the “large” to “small” transformation (at 22°C) which is induced by the addition of 4M NaClO₄. Thus it appears that neutral salts additives in aqueous solutions of polyproline influence both the state of aggregation and the conformation of this polymer.     

Genetic control systems of stem branching and plant height in linseed

A diallel analysis of the traits “plant height”, “number of lateral stems”, and “number of lateral shoots” was carried out using Hayman’s method in three self-pollinated lines and one linear cultivar of linseed. A similarity was demonstrated between the inheritance of the studied traits and the additive-dominant model without any nonallelic interactions. The recessive nature of inheritance of increased plant height and high numbers of shoots together with dominant inheritance of increased numbers of lateral stems was revealed. The number of blocks of polymeric genes responsible for the variability in the studied traits was also estimated. The lines of linseed were ranged according to their contents of dominant alleles.     

The story of stolen chaperones

Prions are self-seeding alternate protein conformations. Most yeast prions contain glutamine/asparagine (Q/N)-rich domains that promote the formation of amyloid-like prion aggregates. Chaperones, including Hsp104 and Sis1, are required to continually break these aggregates into smaller “seeds.” Decreasing aggregate size and increasing the number of growing aggregate ends facilitates both aggregate transmission and growth. Our previous work showed that overexpression of 11 proteins with Q/N-rich domains facilitates the de novo aggregation of Sup35 into the [PSI⁺] prion, presumably by a cross-seeding mechanism. We now discuss our recent paper, in which we showed that overexpression of most of these same 11 Q/N-rich proteins, including Pin4C and Cyc8, destabilized pre-existing Q/N rich prions. Overexpression of both Pin4C and Cyc8 caused [PSI⁺] aggregates to enlarge. This is incompatible with a previously proposed “capping” model where the overexpressed Q/N-rich protein poisons, or “caps,” the growing aggregate ends. Rather the data match what is expected of a reduction in prion severing by chaperones. Indeed, while Pin4C overexpression does not alter chaperone levels, Pin4C aggregates sequester chaperones away from the prion aggregates. Cyc8 overexpression cures [PSI⁺] by inducing an increase in Hsp104 levels, as excess Hsp104 binds to [PSI⁺] aggregates in a way that blocks their shearing.     

Chemical modification of lysine residues in lysozyme may dramatically influence its amyloid fibrillation

Studies on the aggregation of mutant proteins have provided new insights into the genetics of amyloid diseases and the role of the net charge of the protein on the rate, extent, and type of aggregate formation. In the present work, hen egg white lysozyme (HEWL) was employed as the model protein. Acetylation and (separately) citraconylation were employed to neutralize the charge on lysine residues. Acetylation of the lysine residues promoted amyloid formation, resulting in more pronounced fibrils and a dramatic decline in the nucleation time. In contrast, citraconylation produced the opposite effect. In both cases, native secondary and tertiary structures appeared to be retained. Studies on the effect of pH on aggregation suggested greater possibilities for amorphous aggregate formation rather than fibrillation at pH values closer to neutrality, in which the protein is known to take up a conformation more similar to its native form. This is in accord with reports in the literature suggesting that formation of amorphous aggregates is more favored under relatively more native conditions. pH 5 provided a critical environment in which a mixture of amorphous and fibrillar structures were observed. Use of Tango and Aggrescan software which describe aggregation tendencies of different parts of a protein structure suggested critical importance of some of the lysine residues in the aggregation process. Results are discussed in terms of the importance of the net charge in control of protein–protein interactions leading to aggregate formation and possible specific roles of lysine residues 96 and 97.     

Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis

Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP^Sc. Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ～3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP.     

Evidence for lymphocyte chemotaxis toward monocytes during PHA-induced aggregation in vitro

An important, early phenomenon during the development of immune cell interactions in vitro is the formation of multicellular aggregates. We have developed a quantitative assay to determine the kinetics of multicellular aggregate formation within a heterotypic population of cells on a flat surface. This assay follows the time rate of change in the value of an aggregation index for cells in undisturbed culture. For an initial, well-separated population of cells, the index is a minimum and remains at this value if the cells do not move and interact. By contrast, for conditions that promote active cell movement followed by interaction, the index value increases with time. The index, which reflects cells’ relative spatial distributions, is an “indirect enumeration” of the number of cells within aggregates as a function of time. We used this index to follow the aggregative behavior of a population of freshly isolated human peripheral lymphocytes and monocytes. Previous studies have shown that monocytes are centrally located within aggregates and that lymphocytes move to surround monocytes. In order to test if lymphocyte movements are random or directed prior to interactions with monocytes, we formulated a simple model to describe changes in the expected number of cells in an “idealized aggregate” as a function of time. A comparison of the model curves with curves generated from the changes in the aggregation index shows that the best fit derives from a model that involves directed movement of lymphocytes toward monocytes. These results suggest that monocytes produce a chemoattracting agent for lymphocytes for these experimental conditions.     

Sequence Determinants of the Aggregation of Proteins Within Condensates Generated by Liquid-liquid Phase Separation

The transition between the native and amyloid states of proteins can proceed via a deposition pathway via oligomeric intermediates or via a condensation pathway involving liquid droplet intermediates generated through liquid-liquid phase separation. While several computational methods are available to perform sequence-based predictions of the propensity of proteins to aggregate via the deposition pathway, much less is known about the physico-chemical principles that underlie aggregation within condensates. Here we investigate the sequence determinants of aggregation via the condensation pathway, and identify three relevant features: droplet-promoting propensity, aggregation-promoting propensity and multimodal interactions quantified by the binding mode entropy. By using this approach, we show that it is possible to predict aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS). This analysis provides insights into the amino acid code for the conversion of proteins between liquid-like and solid-like condensates.     

Antifibrillizing agents catalyze the formation of unstable intermediate aggregates of beta‐amyloid

Although Alzheimer's disease (AD) is characterized by the extracellular deposition of fibrillar aggregates of beta‐amyloid (Aβ), transient oligomeric species of Aβ are increasingly implicated in the pathogenesis of AD. Natively unfolded monomeric Aβ can misfold and progressively assemble into fibrillar aggregates, following a well‐established “on pathway” seeded‐nucleation mechanism. Here, we show that three simple saccharides, mannose, sucrose, and raffinose, alter Aβ aggregation kinetics and morphology. The saccharides inhibit formation of Aβ fibrils but promote formation of various oligomeric aggregate species through different “off pathway” aggregation mechanisms at 37°C but not at 60°C. The various oligomeric Aβ aggregates formed when coincubated with the different saccharides are morphologically distinct but all are toxic toward SH‐SY5Y human neuroblastoma cells, increasing the level of toxicity and greatly prolonging toxicity compared with Aβ alone. As a wide variety of anti‐Aβ aggregation strategies are being actively pursued as potential therapeutics for AD, these studies suggest that care must be taken to ensure that the therapeutic agents also block toxic oligomeric Aβ assembly as well as inhibit fibril formation. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

In vitro shiro formation between the ectomycorrhizal basidiomycete Tricholoma matsutake and Cedrela herrerae in the Mahogany family (Meliaceae)

Tricholoma matsutake is an ectomycorrhizal basidiomycete that associates with Pinaceae plants, forming a rhizospheric mycelial aggregate called “shiro” from which the prized “matsutake” mushrooms form. Here we document that T. matsutake associates in vitro with Andean Cedrela herrerae (Meliaceae) via root endophyte interactions and efficiently forms shiro. C. herrerae produces many branches, leaves, and lateral roots in association with T. matsutake, unlike C. odorata, which grows in the tropics and produces few leaves and branches in association with the symbiont. This symbiosis may be a unique approach to culturing matsutake as well as to cultivating endangered plant species in vitro.     

A new kinetic scheme for lysozyme refolding and aggregation

The competing first- and third-order reaction scheme for lysozyme is shown to not predict fed-batch lysozyme refolding when the model is parameterized using independent batch experiments, even when variations in chemical composition during the fed-batch experiment are accounted for. A new kinetic scheme is proposed that involves rapid partitioning between the alternative fates of refolding and aggregation, and which allows for aggregation via a sequential mechanism. The model assumes that monomeric lysozyme in different states, including native, is able to aggregate with intermediates, accounting for recent experimental evidence that native protein can be incorporated into aggregates and explaining why native protein in the refolding buffer reduces yield. Stopped-flow light-scattering measurements were used to measure the association rate for the sequential aggregation mechanism, and refolding rate constants were determined in a series of batch experiments designed to be "snapshots" of the composition during a fed-batch experiment. The new kinetic scheme gave a good a priori prediction of fed-batch refolding performance.     

New aspect of the “mycetome” of a thrips,Bactrothrips brevitubus Takahashi (Insecta: Thysanoptera)

Morphology and cytochemical properties of “mycetomes” are described in the developing oocytes and eggs of an idolothripine thrips, Bactrothrips brevitubus (Thysanoptera). The “mycetome” is an aggregation of numerous granules of various sizes. We found no membrane encapsulating the aggregation of granules. Two types of granules are distinguishable: the smaller ones filled with electron-dense material and the larger ones with inclusion of myelin-like structures. Each of the granules has a limiting membrane. The limiting membrane is a simple unit membrane but shows no characteristics of cell walls. No nucleoid or nucleoplasm is detected in the granules. The “mycetome” takes up dyes whose specific incorporation into lysosomes has been demonstrated. In addition, a high activity of acid phosphatase is demonstrated in the “mycetome.” These characteristics apparently indicated that the “mycetome” of Bactrothrips brevitubus is an aggregation of lysosomes but not a clump of microorganisms. Thus we propose that the structure being regarded as the mycetome should be renamed the “lysosomal aggregation.” © 1994 Wiley-Liss, Inc.     

The Diagnosis and Treatment of Arterial Injuries

Repair of arterial injuries has decreased the amputation rate to 15% from 50%, which was prevalent when ligation was practised. Methods of treatment include lateral repair, resection of damaged area with end-to-end anastomosis, and resection and graft, with or without the assistance of partial or complete cardiopulmonary bypass. Lacerations of large arteries (aorta, iliac) may be treated by lateral repair. Lacerations of smaller arteries are best treated by resection and anastomosis, or by resection and graft. True and false aneurysms and arteriovenous fistulas are best treated by resection and restoration of blood flow. “Spasm” in an artery is frequently due to intimal rupture or subintimal hemorrhage, and likewise requires resection and anastomosis in many instances. Clinical examples of each type of injury are presented. Angiography is of great value in establishing the precise abnormality present, its location, the degree of collateral circulation, and the result achieved by surgery.     

Cover Picture: Biotechnology Journal 5/2017

The cover shows a cartoon of wave motion that provides an ideal hydrodynamic environment to induce cell‐cell collision and subsequent aggregation of human mesenchymal stem cells with controlled aggregate size in suspension. The cover is prepared by Ang‐Chen Tsai, Yijun Liu, Xuegang Yuan, Ravindran Chella and Teng Ma authors of the article ”Aggregation kinetics of human mesenchymal stem cells under wave motion“ ( https://doi.org/10.1002/biot.201600448 ).     

Partial amino acid sequence of two forms of human post-gamma-globulin.

We have purified two different electrophoretic forms of Post-γ-globulin defined by electrophoresis as “native slow” form and “fast” form respectively. Amino acid sequences of the first fifty-two residues of the “native slow” form and twenty-nine of the “fast” form were determined. The sequence shows that the “fast” form lacks the first nine amino acids of the “native slow” form.This observation is consistent with the existence of a “native slow” form that is degraded into other more acidic forms of Post-γ-globulin by loss of basic amino acids.     

The distribution of lateral phenotypes in six- to seven-year-old children

An approach to the estimation of the lateral phenotype in children has been developed. During the study, more than 20 lateral phenotypes were identified in six-to seven-year-old children. The most frequent are the following lateral phenotypes: dextrality (motor and sensory), motor dextrality and sensory sinistrality, and motor dextrality and sensory ambidexterity (with a dominant left ear and right eye and with a dominant right ear and left eye). Unilateral left-handers accounted for 0.1% of all children studied; thus, the use of the laterality profile of motor functions as a “marker” of the brain functional asymmetry is rather questionable.     

Aggregation of recombinant hepatitis B surface antigen in Pichia pastoris

The combination of immunoaffinity and size-exclusion chromatography (SEC) is a powerful tool to analyze multiprotein particle assembly. This approach was used to investigate the source of aggregation of recombinant hepatitis B surface antigen (HBsAg) detected in purified material. As HBsAg aggregation does not originate in the stresses, such as the concentration of HBsAg solutions, temperature and chaotropic agents, it is less probable that the HBsAg aggregate is produced during the process. To test whether aggregation takes place in vivo, crude yeast extract containing the expressed HBsAg was fractioned on a Sephacryl S-400 column just after cell disruption, and each fraction immunopurified individually. As a result, the HBsAg aggregate was isolated from a fraction corresponding to the elution of large particle aggregates only, not native HBsAg particles. It was biologically active, which demonstrates aggregate formation by specific assembly of partially or wholly folded HBsAg intermediates.