Fractal symmetry of protein interior: what have we learned?

The application of fractal dimension-based constructs to probe the protein interior dates back to the development of the concept of fractal dimension itself. Numerous approaches have been tried and tested over a course of (almost) 30 years with the aim of elucidating the various facets of symmetry of self-similarity prevalent in the protein interior. In the last 5 years especially, there has been a startling upsurge of research that innovatively stretches the limits of fractal-based studies to present an array of unexpected results on the biophysical properties of protein interior. In this article, we introduce readers to the fundamentals of fractals, reviewing the commonality (and the lack of it) between these approaches before exploring the patterns in the results that they produced. Clustering the approaches in major schools of protein self-similarity studies, we describe the evolution of fractal dimension-based methodologies. The genealogy of approaches (and results) presented here portrays a clear picture of the contemporary state of fractal-based studies in the context of the protein interior. To underline the utility of fractal dimension-based measures further, we have performed a correlation dimension analysis on all of the available non-redundant protein structures, both at the level of an individual protein and at the level of structural domains. In this investigation, we were able to separately quantify the self-similar symmetries in spatial correlation patterns amongst peptide–dipole units, charged amino acids, residues with the π-electron cloud and hydrophobic amino acids. The results revealed that electrostatic environments in the interiors of proteins belonging to ‘α/α toroid’ (all-α class) and ‘PLP-dependent transferase-like’ domains (α/β class) are highly conducive. In contrast, the interiors of ‘zinc finger design’ (‘designed proteins’) and ‘knottins’ (‘small proteins’) were identified as folds with the least conducive electrostatic environments. The fold ‘conotoxins’ (peptides) could be unambiguously identified as one type with the least stability. The same analyses revealed that peptide–dipoles in the α/β class of proteins, in general, are more correlated to each other than are the peptide–dipoles in proteins belonging to the all-α class. Highly favorable electrostatic milieu in the interiors of TIM-barrel, α/β-hydrolase structures could explain their remarkably conserved (evolutionary) stability from a new light. Finally, we point out certain inherent limitations of fractal constructs before attempting to identify the areas and problems where the implementation of fractal dimension-based constructs can be of paramount help to unearth latent information on protein structural properties.     

Scavenger, transducer, RNA chaperone? What ligands of the prion protein teach us about its function

Prion protein, a misfolded isoform of which is the essential component of the agent of prion diseases, still remains an enigmatic protein whose physiological functions are at best hypothetical. To gain a better insight into its putative role, many studies were undertaken to look for molecules that bind prion protein, and have notably identified divalent metal ions, several proteins, and nucleic acids. At first sight, the diversity of prion protein’s ligands seems of little help to infer a plausible function. However, the intrinsically disordered property of its N-terminal tail and the potential of the protein to adopt a transmembrane topology, can both be taken into account to predict its different states during its cellular cycle and its possible functions, of which the most promising correspond to a general scavenger, a sensor or adaptor in a signaling cascade, and an RNA chaperone. Received 16 August 2006; received after revision 7 November 2006; accepted 13 December 2006     

Snake venom action: Are enzymes involved in it?

Summary Enzymes were the first clearly recognized components of snake venoms. When several more were discovered, attempts were made to correlate venom action with enzymic functions. The last few years have seen most successful efforts in the identification, isolation and structural elucidation of highly toxic polypeptides present in snake venoms, in particular of neurotoxins and membrane-active toxins. Following this development the polypeptides were called the true toxic components and the enzymes lost their previous central position in venom pharmacology. The time, therefore, has come to re-evaluate the role of enzymes in the complex interaction between snake and prey. While highly active polypeptides indeed dominate the action of hydrophiid venoms, they appear to play a lesser role in crotalid venom action as compared with enzyme components. Enzymes are involved in many levels of venom action, e. g. by serving as spreading factors, of by producing very active agents, such as bradykinin and lysolecithins in tissues of preys or predators. Some toxins, e. g. the membrane-active polypeptides appear to participate in the interaction between membrane phospholipids and venom phospholipases. The classical neurotoxin, -bungarotoxin, has been recognized as a powerful phospholipase. Several instances are known which indicate that some enzymes potentiate the toxic action of others; the analysis of a single enzyme may, therefore, not fully reveal its biofunction. For 3 enzymes, ophidianl-amino acid oxidase, ATPpyrophosphatase, and acetylcholinesterase, some of the problems pertaining to venom toxicity are discussed.     

Silent performances: Are “repertoires” really post-Kuhnian?

Ankeny and Leonelli (2016) propose “repertoires” as a new way to understand the stability of certain research programs as well as scientific change in general. By bringing a more complete range of social, material, and epistemic elements into one framework, they position their work as a correction to the Kuhnian impulse in philosophy of science and other areas of science studies. I argue that this “post-Kuhnian” move is not complete, and that repertoires maintain an internalist perspective. Comparison with an alternative framework, the “sociotechnical imaginaries” of Jasanoff and Kim (2015), illustrates precisely which elements of practice are externalized by Ankeny and Leonelli. Specifically, repertoires discount the role of audience, without whom the repertoires of science are unintelligible, and lack an explicit place for ethical and political imagination, which provide meaning for otherwise mechanical promotion of particular research programs. This comparison reveals, I suggest, two distinct modes of scholarship, one internalist and the other critical. While repertoires can be modified to meet the needs of critical STS scholars and to completely reject Kuhn's internalism, whether or not we do so depends on what we want our scholarship to achieve.     

The cold case: Are rhinoviruses perfectly adapted pathogens?

Rhinoviruses, which cause common cold, belong to the Picornaviridae family, small non-enveloped viruses (diameter 15-30 nm) containing a single-stranded RNA genome (about 7 kb). Over 100 different rhinoviral serotypes have been identified thus far, establishing rhinoviruses as the most diverse group of Picornaviridae. Based on receptor binding properties, rhinoviruses are divided into two classes: the major group binding to intracellular adhesion molecule-1 and the minor group binding to the very low density lipoprotein receptors. Interactions between virus and the receptor molecules cause a conformational change in the capsid, which is a prerequisite for viral uptake. Rhinoviruses trigger a chemokine response upon infection that may lead to exacerbation of the symptoms of common cold, i.e. asthma and inflammation. The following review aims to summarize the knowledge about rhinoviral infections and discusses therapeutical approaches against this almost perfectly adapted pathogen.     

Aluminium in Alzheimer’s disease: are we still at a crossroad?

Aluminium, an environmentally abundant non-redox trivalent cation has long been implicated in the pathogenesis of Alzheimers disease (AD). However, the definite mechanism of aluminium toxicity in AD is not known. Evidence suggests that trace metal homeostasis plays a crucial role in the normal functioning of the brain, and any disturbance in it can exacerbate events associated with AD. The present paper reviews the scientific literature linking aluminium with AD. The focus is on aluminium levels in brain, region-specific and subcellular distribution, its relation to neurofibrillary tangles, amyloid beta, and other metals. A detailed mechanism of the role of aluminium in oxidative stress and cell death is highlighted. The importance of complex speciation chemistry of aluminium in relation to biology has been emphasized. The debatable role of aluminium in AD and the cross-talk between aluminium and genetic susceptibility are also discussed. Finally, it is concluded based on extensive literature that the neurotoxic effects of aluminium are beyond any doubt, and aluminium as a factor in AD cannot be discarded. However, whether aluminium is a sole factor in AD and whether it is a factor in all AD cases still needs to be understood.Received 22 July 2004; received after revision 3 September 2004; accepted 16 September 2004     

On glioblastoma and the search for a cure: where do we stand?

Although brain tumours have been documented and recorded since the nineteenth century, 2016 marked 90 years since Percival Bailey and Harvey Cushing coined the term “glioblastoma multiforme”. Since that time, although extensive developments in diagnosis and treatment have been made, relatively little improvement on prognosis has been achieved. The resilience of GBM thus makes treating this tumour one of the biggest challenges currently faced by neuro-oncology. Aggressive and robust development, coupled with difficulties of complete resection, drug delivery and therapeutic resistance to treatment are some of the main issues that this nemesis presents today. Current treatments are far from satisfactory with poor prognosis, and focus on palliative management rather than curative intervention. However, therapeutic research leading to developments in novel treatment stratagems show promise in combating this disease. Here we present a review on GBM, looking at the history and advances which have shaped neurosurgery over the last century that cumulate to the present day management of GBM, while also exploring future perspectives in treatment options that could lead to new treatments on the road to a cure.     

Short‐term forecasts of economic activity: Are fortnightly factors useful?

A short‐term mixed‐frequency model is proposed to estimate and forecast Italian economic activity fortnightly. We introduce a dynamic one‐factor model with three frequencies (quarterly, monthly, and fortnightly) by selecting indicators that show significant coincident and leading properties and are representative of both demand and supply. We conduct an out‐of‐sample forecasting exercise and compare the prediction errors of our model with those of alternative models that do not include fortnightly indicators. We find that high‐frequency indicators significantly improve the real‐time forecasts of Italian gross domestic product (GDP); this result suggests that models exploiting the information available at different lags and frequencies provide forecasting gains beyond those based on monthly variables alone. Moreover, the model provides a new fortnightly indicator of GDP, consistent with the official quarterly series.     

State of the field: Are the results of science contingent or inevitable?

This paper presents a survey of the literature on the problem of contingency in science. The survey is structured around three challenges faced by current attempts at understanding the conflict between “contingentist” and “inevitabilist” interpretations of scientific knowledge and practice. First, the challenge of definition: it proves hard to define the positions that are at stake in a way that is both conceptually rigorous and does justice to the plethora of views on the issue. Second, the challenge of distinction: some features of the debate suggest that the contingency issue may not be sufficiently distinct from other philosophical debates to constitute a genuine, independent philosophical problem. And third, the challenge of decidability: it remains unclear whether and how the conflict could be settled on the basis of empirical evidence from the actual history of science. The paper argues that in order to make progress in the present debate, we need to distinguish more systematically between different expressions that claims about contingency and inevitability in science can take. To this end, it introduces a taxonomy of different contingency and inevitability claims. The taxonomy has the structure of an ordered quadruple. Each contingency and each inevitability claim contains an answer to the following four questions: (how) are alternatives to current science possible, what types of alternatives are we talking about, how should the alternatives be assessed, and how different are they from actual science?     

Poincaréan intuition revisited: what can we learn from Kant and Parsons?

This paper provides a comprehensive critique of Poincaré’s usage of the term intuition in his defence of the foundations of pure mathematics and science. Kant’s notions of sensibility and a priori form and Parsons’s theory of quasi-concrete objects are used to impute rigour into Poincaré’s interpretation of intuition. In turn, Poincaré’s portrayal of sensible intuition as a special kind of intuition that tolerates the senses and imagination is rejected. In its place, a more harmonized account of how we perceive concrete objects is offered whereby intuitive knowledge is consistently a priori whatever the domain of application.     

Glycoconjugates in sperm function and gamete interactions: how much sugar does it take to sweet-talk the egg?

Glycoconjugates in the mammalian reproductive tract are critical components of the molecular mechanisms that control sperm maturation, sperm transport and gamete interactions. In the oviduct of many species, sperm transport and maturation are regulated by protein-carbohydrate interactions that form a sperm reservoir. Subsequently, gamete interactions are mediated by the binding of lectin-like sperm proteins with carbohydrate moieties on the zona pellucida. The sperm glycocalyx is extensively modified during sperm transport and maturation. Multiple functions have been proposed for this dense carbohydrate layer overlying the sperm plasmalemma, and sperm-surface carbohydrates have been implicated in immune-mediated human infertility. The structure and function of glycoconjugates in the oviductal sperm reservoir, the zona pellucida, and on the sperm surface are reviewed.     

Going Up–Going Down: How Good Are People at Forecasting Trends and Changes in Trends?

Prior studies of judgemental time-series forecasting have found that people have problems with downward-sloping series. This laboratory-based study presents a controlled experiment of series direction and it investigates the problems of changing trends. Results confirm that people have significant difficulties in dealing with downward-sloping series and that behaviour is consistent with a general tendency to anticipate that downward series will reverse themselves. There is a significantly less tendency to do so for upward series. Results are discussed in terms of systematic and unsystematic error.© 1997 John Wiley & Sons, Ltd.     

Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding?

Using a set of 372 proteins representative of a variety of 56 distinct globular folds, a statistical correlation was observed between two recently revealed features of protein structures: tightened end fragments or 'closed loops', i. e. sequence fragments that are able in three-dimensional (3D) space to nearly close their ends (a current parameter of polymer physics), and 'topohydrophobic positions', i. e. positions always occupied in 3D space by strong hydrophobic amino acids for all members of a fold family. Indeed, in sequence space, the distribution of preferred lengths for tightened end fragments and that for topohydrophobic separation match. In addition to this statistically significant similarity, the extremities of these 'closed loops' may be preferentially occupied by topohydrophobic positions, as observed on a random sample of various folds. This observation may be of special interest for sequence comparison of distantly related proteins. It is also important for the ab initio prediction of protein folds, considering the remarkable topological properties of topohydrophobic positions and their paramount importance within folding nuclei. Consequently, topohydrophobic positions locking the 'closed loops' belong to the deep cores of protein domains and might have a key role in the folding process. Received 1 February 2001; accepted 7 February 2001     

<Emphasis Type="Italic">Trichomonas vaginalis</Emphasis> degrades nitric oxide and expresses a flavorubredoxin-like protein: a new pathogenic mechanism?

Besides possessing many physiological roles, nitric oxide (NO) produced by the immune system in infectious diseases has antimicrobial effects. Trichomoniasis, the most widespread non-viral sexually transmitted disease caused by the microaerophilic protist Trichomonas vaginalis, often evolves into a chronic infection, with the parasite able to survive in the microaerobic, NO-enriched vaginal environment. We relate this property to the finding that T. vaginalis degrades NO under anaerobic conditions, as assessed amperometrically. This activity, which is maximal (133 ± 41 nmol NO/10⁸ cells per minute at 20°C) at low NO concentrations ( 1.2 M), was found to be: (i) NADH dependent, (ii) cyanide insensitive and (iii) inhibited by O₂. These features are consistent with those of the Escherichia coli A-type flavoprotein (ATF), recently discovered to be endowed with NO reductase activity. Using antibodies against the ATF from E. coli, a protein band was immunodetected in the parasite grown in a standard medium. If confirmed, the expression of an ATF in eukaryotes suggests that the genes coding for ATFs were transferred during evolution from anaerobic Prokarya to pathogenic protists, to increase their fitness for the microaerobic, parasitic life style. Thus the demonstration of an ATF in T. vaginalis would appear relevant to both pathology and evolutionary biology. Interestingly, genomic analysis has recently demonstrated that Giardia intestinalis and other pathogenic protists have genes coding for ATFs.Received 1 November 2003; received after revision 5 January 2004; accepted 13 January 2004