Loop Fold Structure of Proteins: Resolution of Levinthal's Paradox

Abstract

According to Levinthal a protein chain of ordinary size would require enormous time to sort its conformational states before the final fold is reached. Experimentally observed time of folding suggests an estimate of the chain length for which the time would be sufficient. This estimate by order of magnitude fits to experimentally observed universal closed loop elements of globular proteins—25–30 residues.     

Biotic resistance to invasion is ubiquitous across ecosystems of the United States

The biotic resistance hypothesis predicts that diverse native communities are more resistant to invasion. However, past studies vary in their support for this hypothesis due to an apparent contradiction between experimental studies, which support biotic resistance, and observational studies, which find that native and non‐native species richness are positively related at broad scales (small‐scale studies are more variable). Here, we present a novel analysis of the biotic resistance hypothesis using 24 456 observations of plant richness spanning four community types and seven ecoregions of the United States. Non‐native plant occurrence was negatively related to native plant richness across all community types and ecoregions, although the strength of biotic resistance varied across different ecological, anthropogenic and climatic contexts. Our results strongly support the biotic resistance hypothesis, thus reconciling differences between experimental and observational studies and providing evidence for the shared benefits between invasive species management and native biodiversity conservation.     

The mitonuclear compatibility hypothesis of sexual selection

Why females assess ornaments when choosing mates remains a central question in evolutionary biology. We hypothesize that the imperative for a choosing female to find a mate with nuclear oxidative phosphorylation (OXPHOS) genes that are compatible with her mitochondrial OXPHOS genes drives the evolution of ornaments. Indicator traits are proposed to signal the efficiency of OXPHOS function thus enabling females to select mates with nuclear genes that are compatible with maternal mitochondrial genes in the formation of OXPHOS complexes. Species-typical pattern of ornamentation is proposed to serve as a marker of mitochondrial type ensuring that females assess prospective mates with a shared mitochondrial background. The mitonuclear compatibility hypothesis predicts that the production of ornaments will be closely linked to OXPHOS pathways, and that sexual selection for compatible mates will be strongest when genes for nuclear components of OXPHOS complexes are Z-linked. The implications of this hypothesis are that sexual selection may serve as a driver for the evolution of more efficient cellular respiration.     

Protein folding and the order/disorder paradox

Most proteins encoded by the nuclear genome are synthesized in the cytoplasm and fold into precise 3D structures. During synthesis, the nascent polypeptide begins to fold as it traverses the large subunit of the ribosome and is assisted by molecular chaperones in attaining its precise folded/highly ordered state efficiently and in a biologically relevant timescale. Proteins that are misfolded are culled, re-routed, and marked by mechanisms such as ubiquitinylation for degradation ensuring strict quality control (QC). In addition to the highly ordered "globular" proteins, emerging evidence indicates that a large fraction of the proteome also comprises the so-called "Intrinsically Disordered Proteins" (IDPs). IDPs are proteins that lack rigid 3D structures and instead, exist as dynamic ensembles. The dynamic structures in the IDPs have many similarities with "normal" globular proteins such as the native (ordered), and non-native (molten globule, pre-molten globule, and coil-like) states seen during folding of "normal" globular proteins. However, unlike the case of the nascent globular proteins, IDPs evade being detected as "misfolded" and degraded by the cell's QC system. We refer to this paradox as the order/disorder paradox and postulate that the IDPs capitalize on their intrinsic promiscuity and ability to undergo disorder-to-order transitions upon binding to biological targets (coupled folding and binding) to escape the cell's surveillance machinery. Understanding the mechanism by which the IDPs evade the quality check has wide implications from protein folding to disease biology since the aggregation of misfolded proteins underlies several debilitating illnesses such as many neurodegenerative diseases and cancer.     

Multiple aspects of condition influence a heritable sexual trait: a synthesis of the evidence for capture of genetic variance in red junglefowl

A long‐standing question in the study of sexual selection is: if an attractive male trait signals heritable aspects of quality, how does genetic variation associated with that trait persist in the face of directional selection? It has been proposed that sensitivity to condition in general could allow a sexual signal to show heritable variation even under persistent directional selection. The multitude of genes underlying components of condition present a large target for mutation, and so genetic variance in condition may not be readily exhausted by selection. Insights gained in studies of the red junglefowl are relevant to this hypothesis, and provide a model for research in other systems. The fleshy comb of male red junglefowl is among the best‐studied sexual signals. Multiple components of condition, such as health, immune function, testosterone, and social status, influence comb growth, and, in the present study, we provide the first comprehensive integration of this large body of evidence to lay out the compelling case for condition‐dependence of the junglefowl comb. Variation in comb size is heritable and, most important to this issue, is genetically correlated with heritable variation in a body condition index. Although understanding of the red junglefowl's comb is far from complete, it exceeds our understanding of many other sexual signals and provides an empirical model for the study of condition‐dependent signals in general. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 651–660.     

An ironic reductio for a 'pro-life' argument: Hurlbut's proposal for stem cell research

William Hurlbut, a Stanford University bioethicist and member of the President's Council on Bioethics, recently proposed a solution to the current impasse over human embryonic stem cell research in the United States. He suggested that researchers could use genetic engineering and somatic cell nuclear transfer (i.e. cloning) to develop human 'pseudo-embryos' that have no potential to develop fully into human persons. According to Hurlbut, even thinkers who typically ascribe high moral status to human embryos could approve of destroying these 'pseudo-embryos' for the sake of harvesting human embryonic stem cells. This essay argues, first, that an argument based on the 'paradox of the heap' (an argument that many 'pro-life' thinkers employ in order to defend the notion that human embryos have high moral value from the moment of conception) challenges the ethical legitimacy of Hurlbut's proposal. Second, the paper argues that this conflict may illustrate a reductio ad absurdum for this 'pro-life' argument itself rather than being a problem for Hurlbut's proposal. As a result, the paper challenges the 'pro-life'strategy of arguing that one should respond to uncertainty about the moral status of developing embryos by being morally 'cautious' and granting all human embryos full moral status from the moment of conception. It appears that one is faced with a complex series of choices (about where to draw the moral line between entities that are human persons and entities that are not), and a strict moral 'cautiousness' about this series of choices may ultimately lead to absurdity.     

A potential resolution to the lek paradox through indirect genetic effects

Females often prefer males with elaborate traits, even when they receive no direct benefits from their choice. In such situations, mate discrimination presumably has genetic advantages; selective females will produce offspring of higher genetic quality. Over time, persistent female preferences for elaborate secondary-sexual traits in males should erode genetic variance in these traits, eventually eliminating any benefit to the preferences. Yet, strong female preferences persist in many taxa. This puzzle is called the lek paradox and raises two primary questions: do females obtain genetic benefits for offspring by selecting males with elaborate secondary-sexual characteristics and, if so, how is the genetic variation in these male traits maintained? We suggest that indirect genetic effects may help to resolve the lek paradox. Maternal phenotypes, such as habitat selection behaviours and offspring provisioning, often influence the condition and the expression of secondary-sexual traits in sons. These maternal influences are commonly genetic based (i.e. they are indirect genetic effects). Females choosing mates with elaborate traits may receive ‘good genes’ for daughters in the form of effective maternal characteristics. Recognizing the significance of indirect genetic effects may be important to our understanding of the process and consequences of sexual selection.     

Positive Association Among Three Binary Variables and Cross-Product Ratios

We show that, when the three-way association level among thethree binary variables, X, U₁ and U₂ is fixed, D_P = pr(X = 1¦U₁= 1) – pr(X = 1¦U₁ = 0) increases as the cross-productratio of U₁ and U₂ increases under the assumption that X ispositively associated with U₁ and U₂. We then discuss some implicationsof this property.     

Discrete genetic variation in mate choice and a condition-dependent preference function in the side-blotched lizard: implications for the formation and maintenance of coadapted gene complexes

Variation in female preference functions, both genotypic andphenotypic, has been largely ignored in the literature, despiteits implications to the maintenance of genetic variation inpopulations and the resolution of the "Lek paradox." Polymorphicpopulations, such as in the side-blotched lizard, provide idealstudy systems for its investigation, especially in the contextof incipient processes of sympatric speciation. Females of theside blotch lizard exist in 2 genetically distinct morphs, yellowthroated and orange throated, that experience disruptive selectionfor life history traits. Males express 3 throat color morphs,blue, orange, and yellow, that exhibit alternative strategiesin intrasexual competition. We experimentally tested for femalepreference in triadic mate choice trials to identify the presenceof discrete genetic and condition-dependent variation in femalepreference function. We found that females did in fact showgenetic variation in preference for males but that females alsooperate a multicondition preference function dependent uponthe genotype of the female and her state (number of clutcheslaid). Females exhibited positive assortative mating prior tothe first clutch. However, prior to later clutches, orange femalesswitched choice, preferring yellow males. These findings arediscussed in relation to the maintenance of coadapted gene complexeswithin populations and the prevention of divergent directionalselection (population bifurcation) by condition-dependent variationin mate choice.