The posttranslational concept of protein folding: how valid is it?

Two concepts of protein folding are known. One of them, the cotranslational concept, states that a protein folds during the synthesis of the polypeptide chain on the ribosome. According to the other, the posttranslational concept, the protein starts to fold just after the synthesis of its polypeptide chain. This article attempts to show that the posttranslational concept is hardly suited to solve the problem of protein folding. In our opinion, polypeptide chains cannot be represented as random coils. They are stiff chain-like macromolecules rather than flexible ones: the single bond rotational barriers of a polypeptide substantially exceed the accepted standard values; even in strong denaturing conditions, a protein possesses a considerable amount of residual folded structures. We believe that the popular "hierarchical" models for the protein folding mechanism are not realistic because the formation of secondary and tertiary structures of proteins occurs simultaneously and cooperatively. The time for the elongation of a polypeptide chain by one amino acid residue during biosynthesis exceeds considerably the time of the formation of alpha-helices and beta-sheets in proteins as well as the time supposed for the spatial structure formation of a native protein during renaturation. Thus, we believe that the mechanism of protein folding in vivo cannot be clarified by denaturation-renaturation experiments. In our opinion, the phenomenon of protein renaturation is no more than the restoration of native protein conformation (which initially forms cotranslationally) disrupted during denaturation, and thus denaturation-renaturation experiments cannot serve as a model to clarify the mechanism of protein folding.     

Paternal obesity: how bad is it for sperm quality and progeny health?

There is substantial evidence that paternal obesity is associated not only with an increased incidence of infertility, but also with an increased risk of metabolic disturbance in adult offspring. Apparently, several mechanisms may contribute to the sperm quality alterations associated with paternal obesity, such as physiological/hormonal alterations, oxidative stress, and epigenetic alterations. Along these lines, modifications of hormonal profiles namely reduced androgen levels and elevated estrogen levels, were found associated with lower sperm concentration and seminal volume. Additionally, oxidative stress in testis may induce an increase of the percentage of sperm with DNA fragmentation. The latter, relate to other peculiarities such as alteration of the embryonic development, increased risk of miscarriage, and development of chronic morbidity in the offspring, including childhood cancers. Undoubtedly, epigenetic alterations (ie, DNA methylation, chromatin modifications, and small RNA deregulation) of sperm related to paternal obesity and their consequences on the progeny are poorly understood determinants of paternal obesity-induced transmission. In this review, we summarize and discuss the data available in the literature regarding the biological, physiological, and molecular consequences of paternal obesity on male fertility potential and ultimately progeny health.     

Proximate and ultimate causes: how come? and what for?

Proximate and ultimate causes in evolutionary biology have come to conflate two distinctions. The first is a distinction between immediate and historical causes. The second is between explanations of mechanism and adaptive function. Mayr emphasized the first distinction but many evolutionary biologists use proximate and ultimate causes to refer to the second. I recommend that ‘ultimate cause’ be abandoned as ambiguous.     

Quantitative modeling in cell biology: what is it good for?

Recently, there has been a surge in the number of pioneering studies combining experiments with quantitative modeling to explain both relatively simple modules of molecular machinery of the cell and to achieve system-level understanding of cellular networks. Here we discuss the utility and methods of modeling and review several current models of cell signaling, cytoskeletal self-organization, nuclear transport, and the cell cycle. We discuss successes of and barriers to modeling in cell biology and its future directions, and we argue, using the field of bacterial chemotaxis as an example, that the closer the complete systematic understanding of cell behavior is, the more important modeling becomes and the more experiment and theory merge.     

Hysteresis and cell cycle transitions: how crucial is it?

Recently, experiments have shown that cyclin-dependent kinase (CDK) activity exhibits hysteresis in its response to total cyclin when cyclin is made nondegradable and controlled externally. This observation was taken to support mathematical modeling predictions regarding the underlying dynamics of the cell cycle. However, cell cycle dynamics can also be generated by other nonhysteretic mechanisms. To examine the robustness of the hysteretic response of CDK activity to total cyclin, we simulated various cell cycle signal transduction networks, and correlated the dynamics to the response function of CDK activity versus total cyclin. By randomly searching the parameter space, we assessed robustness by estimating the frequency of hysteretic versus nonhysteretic dynamical mechanisms. When the dynamical instabilities were caused by feedback loops in CDK phosphorylation and dephosphorylation or by feedback between cyclin and the CDK inhibitor, the response function of CDK activity versus total cyclin correlated well with the dynamical instabilities. However, when the dynamical instabilities originated from feedback between cyclin and APC-CDH1 or RB-E2F, the response function did not correlate with dynamical instabilities. Thus, although a hysteretic response is neither necessary nor sufficient, it is in general a much more robust mechanism for generating cell cycle dynamics than nonhysteretic mechanisms.     

Microtubules and cellulose microfibrils: how intimate is their relationship?

The recent visualization of the motion of fluorescently labeled cellulose synthase complexes by Alexander Paredez and colleagues heralds the start of a new era in the science of the plant cell wall. Upon drug-induced complete depolymerization, the movement of the complexes does not become disordered but instead establishes an apparently self-organized novel pattern. The ability to label complexes in vivo has provided us with the ideal tool for tackling the intriguing question of the underlying default mechanisms at play.     

Hypochlorous acid-mediated protein oxidation: how important are chloramine transfer reactions and protein tertiary structure?

Hypochlorous acid (HOCl) is a powerful oxidant generated from H2O2 and Cl- by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that occurs in numerous human pathologies. As proteins and amino acids are highly abundant in vivo and react rapidly with HOCl, they are likely to be major targets for HOCl. In this study, two small globular proteins, lysozyme and insulin, have been oxidized with increasing excesses of HOCl to determine whether the pattern of HOCl-mediated amino acid consumption is consistent with reported kinetic data for isolated amino acids and model compounds. Identical experiments have been carried out with mixtures of N-acetyl amino acids (to prevent reaction at the alpha-amino groups) that mimic the protein composition to examine the role of protein structure on reactivity. The results indicate that tertiary structure facilitates secondary chlorine transfer reactions of chloramines formed on His and Lys side chains. In light of these data, second-order rate constants for reactions of Lys side chain and Gly chloramines with Trp side chains and disulfide bonds have been determined, together with those for further oxidation of Met sulfoxide by HOCl and His side chain chloramines. Computational kinetic models incorporating these additional rate constants closely predict the experimentally observed amino acid consumption. These studies provide insight into the roles of chloramine formation and three-dimensional structure on the reactions of HOCl with isolated proteins and demonstrate that kinetic models can predict the outcome of HOCl-mediated protein oxidation.     

Blood-bank testing for infectious diseases: how safe is blood transfusion?

Remarkable progress has been made in transfusion safety from infection over the past three decades. Donor deferrals for at-risk behaviors, the introduction of more-sensitive viral-screening assays and the recent introduction of nucleic-acid amplification technology have nearly eliminated transmission of HIV and hepatitis C virus (HCV) by blood transfusion in North America. Nevertheless, risks of other infectious agents for which such robust screening tools have not been developed, such as bacteria and parasites, still remain. As a result of these successes, the non-infectious risks such as misidentification of patients and inadequate and inappropriate transfusion have become the primary sources of transfusion risk.     

Single-molecule biology: what is it and how does it work?

Biochemistry and structural biology are undergoing a dramatic revolution. Until now, we have tried to study subtle and complex biological processes by crude in vitro techniques, looking at average behaviors of vast numbers of molecules under conditions usually remote from those existing in the cell. Researchers have realized the limitations of this approach, but none other has been available. Now, we can not only observe the nuances of the behaviors of individual molecules but prod and probe them as well. Perhaps most important is the emerging ability to carry out such observations and manipulations within the living cell. The long-awaited leap to an in vivo biochemistry is at last underway.     

The insulin-receptor interaction: is the kinetic approach for inferring negative-cooperative site-site interactions valid?

The dissociation of insulin from its receptor is reportedly enhanced when the dissociation is induced by dilution in the presence of insulin. This experiment is frequently conducted when curvilinear Scatchard plots of insulin binding are observed in order to infer negative cooperative site-site interactions amongst insulin receptors. However, when insulin binding to purified liver plasma membranes was measured at 15 degrees C in 50 mM Tris, pH 7.5 containing 0.1% bovine serum albumin and 100 U/ml bacitracin, the insulin binding data was characterised by a linear Scatchard plot and a Hill plot with a slope equal to unity. Thus, under the conditions of this binding assay, insulin apparently bound to a single non-interacting class of homogeneous binding sites. But, despite the apparent absence of cooperative interactions under these specific conditions, the dissociation of receptor-bound insulin was still enhanced when the dissociation of insulin from its receptor was induced by dilution in the presence of insulin. This result cast serious doubt on the validity of inferring negative-cooperative site-site interactions amongst insulin receptors based solely on the observation that the dissociation of receptor-bound insulin is enhanced by dilution in the presence of insulin.     

Assessment of variability in biomass yield and quality: what is an adequate size of sampling area for miscanthus?

To diversify energy crop production and improve its biodiversity and sustainability, there is currently a search for alternative energy crops. Many of the newly arising alternatives are perennial species such as the C₄ grass miscanthus. The assessment of reliable data is a prerequisite for understanding the performance of these crops and developing corresponding management systems. However there is great uncertainty concerning research methodology for these crops. When data are collected from small plots of perennial crops, such as miscanthus or short rotation coppice plantations, a larger variability is expected than for cereals. A square meter cut, corresponding to harvest practice in cereals, is not sufficient for perennial C₄ grasses and is not recommended for these species. The aim of this research was to identify an adequate size of sampling area for miscanthus to estimate the true biomass yield or quality. For this purpose, whole plots of 10‐ and 14‐year old miscanthus stands were divided into smaller subplots. These were used to calculate variances for various sizes of simulated plots. The variances for all traits in the experiments were rather high when the sampling area was smaller than 2 m². A cutting regime of more than 5.6 m² would be advisable, but an area of 3 m² is sufficient to eliminate approximately 90% of the variances and is therefore an adequate size of sampling area.     

Low-dose effects and biphasic effect profiles: is trenbolone a genotoxicant?

Over the last years, extensive research has documented endocrine-disrupting activities for a significant number of substances including, among others, hormones, pharmaceuticals, pesticides and surfactants. Nonetheless, for most endocrine disruptors, toxicological profiles are still incomplete or even lacking. A systematic review has shown that a number of endocrine disruptors with steroid-modulating effects may also exert mutagenic and carcinogenic activities. For trenbolone, an androgenic compound, there is controversy about its genotoxic properties in the literature, apparently with a strong dependence on the choice of the test system. Since fish and other aquatic animals are at risk of exposure to run-offs from cattle feedlots or sewage-discharge sites containing trenbolone, potential consequences to aquatic ecosystems need to be assessed. To this end, the potential genotoxic hazard of trenbolone was tested in vitro in the permanent rainbow trout-liver cell-line RTL-W1, as well as in primary cell cultures derived from zebrafish (Danio rerio) embryos after in vivo exposure. In either test system, a potential genotoxic hazard characterized by biphasic dose-response curves could be documented even at exposure concentrations of 30μg/L. These results thus confirm the conclusion that the steroid trenbolone may act as a genotoxic substance.     

Collagen-induced arthritis and related animal models: how much of their pathogenesis is auto-immune, how much is auto-inflammatory?

In this review, we discuss our studies on the pathogenesis of collagen-induced arthritis (CIA) and related mouse models for rheumatoid arthritis. Of note, these models invariably rely on the use of complete Freund's adjuvant (CFA). Our analysis has focused on explaining the dichotomous - either protective or disease-promoting - role of endogenous IFN-γ. Induction of a myelopoietic burst by CFA was identified as an important and underestimated factor in mediating the role of IFN-γ and other cytokines (IL-6, IL-17, GCP-2, RANK-L). Myelopoiesis provides an excess in precursors for joint-infiltrating neutrophils and osteoclasts. We postulate that classical CIA is primarily an auto-inflammatory disease, in part because of a strong innate immune response to the adjuvant. Superimposed on this, collagen-specific auto-immunity reinforces inflammatory reactivity in joints.     

Activation loop phosphorylation and catalysis in protein kinases: is there functional evidence for the autoinhibitor model?

Many protein kinases are activated strongly by the phosphorylation of a polypeptide region (activation loop) that lies outside the active-site cleft. Analysis of the X-ray crystallographic structures of the insulin receptor with the activation loop in the phosphorylated and dephosphorylated forms offers a testable model for the mechanism of activity regulation by the loop. In this model, the dephosphorylated activation loop can act as an autoinhibitor by blocking substrate access to the active site. Phosphorylation of the loop could then release the autoinhibitor from the active site, allowing substrate binding and catalysis. While this model has been widely invoked, it was not clear if solution studies would support an autoinhibitory model for kinase regulation, in general. We review the results of solution studies on six protein kinases that test the role of the activation loop in controlling active-site access. While loop phosphorylation enhances substrate binding in two cases, four protein kinases display little or no effect on substrate dissociation constants. By comparison, phosphorylation increases catalysis by 2-4 orders of magnitude in all cases. These findings can be used to place the phosphorylatable activation loops into two broad, functional subcategories. (i) Gated activation loops exhibit bifunctional properties restricting substrate access and controlling catalysis. (ii) Nongated activation loops allow free movement of the substrate in and out of the active site irrespective of phosphorylation state but potently modulate the phosphoryl transfer step. Thus, while activation loop phosphorylation greatly modulates catalytic potential, it does not necessarily affect substrate binding, as once widely believed.