Mechanistic insights into the role of Hop2–Mnd1 in meiotic homologous DNA pairing

The Hop2–Mnd1 complex functions with the DMC1 recombinase in meiotic recombination. Hop2–Mnd1 stabilizes the DMC1-single-stranded DNA (ssDNA) filament and promotes the capture of the double-stranded DNA partner by the recombinase filament to assemble the synaptic complex. Herein, we define the action mechanism of Hop2–Mnd1 in DMC1-mediated recombination. Small angle X-ray scattering analysis and electron microscopy reveal that the heterodimeric Hop2–Mnd1 is a V-shaped molecule. We show that the protein complex harbors three distinct DNA binding sites, and determine their functional relevance. Specifically, the N-terminal double-stranded DNA binding functions of Hop2 and Mnd1 co-operate to mediate synaptic complex assembly, whereas ssDNA binding by the Hop2 C-terminus helps stabilize the DMC1-ssDNA filament. A model of the Hop2-Mnd1-DMC1-ssDNA ensemble is proposed to explain how it mediates homologous DNA pairing in meiotic recombination.     

Right or left turn? RecA family protein filaments promote homologous recombination through clockwise axial rotation

The RecA family proteins mediate homologous recombination, a ubiquitous mechanism for repairing DNA double-strand breaks (DSBs) and stalled replication forks. Members of this family include bacterial RecA, archaeal RadA and Rad51, and eukaryotic Rad51 and Dmc1. These proteins bind to single-stranded DNA at a DSB site to form a presynaptic nucleoprotein filament, align this presynaptic filament with homologous sequences in another double-stranded DNA segment, promote DNA strand exchange and then dissociate. It was generally accepted that RecA family proteins function throughout their catalytic cycles as right-handed helical filaments with six protomers per helical turn. However, we recently reported that archaeal RadA proteins can also form an extended right-handed filament with three monomers per helical turn and a left-handed protein filament with four monomers per helical turn. Subsequent structural and functional analyses suggest that RecA family protein filaments, similar to the F1-ATPase rotary motor, perform ATP-dependent clockwise axial rotation during their catalytic cycles. This new hypothesis has opened a new avenue for understanding the molecular mechanism of RecA family proteins in homologous recombination.     

Can glutamine and growth hormone promote protein anabolism in children with cystic fibrosis?

To determine whether recombinant human growth hormone (rhGH), glutamine (GLN) or a combination of both agents can enhance protein synthesis in cystic fibrosis (CF) patients, six 9.6 +/- 0.5-year-old prepubertal children (4 M, 2 F) with CF and stable lung disease with undernutrition (weight/height <50th percentile) or delayed growth (height <5th percentile) received stable isotope infusions, in the postabsorptive state and on 4 separate study days: (a) at baseline, and after a 4-week treatment with either, (b) oral GLN (0.7 g/kg/day), (c) rhGH (0.3 mg/kg/week, SC), or (d) both GLN and rhGH. Four-hour infusions of (13)C-leucine were used to assess leucine appearance rate (Ra, an index of protein breakdown), oxidation (Ox), and non-oxidative leucine disposal (NOLD, an index of protein synthesis). Results are expressed as changes (%) from baseline:We conclude that in children with CF: (1) due to high inter-subject variability, oral glutamine does not significantly enhance protein gain; (2) rhGH has significant anabolic effects which are mediated by stimulation of protein synthesis, and (3) glutamine does not enhance the effect of rhGH.     

Can cytoplasmic incompatibility inducing Wolbachia promote the evolution of mate preferences?

The maternally inherited bacterium, Wolbachia pipientis, manipulates host reproduction by rendering uninfected females reproductively incompatible with infected males (cytoplasmic incompatibility, CI). Hosts may evolve mechanisms, such as mate preferences, to avoid fitness costs of Wolbachia infection. Despite the potential importance of mate choice for Wolbachia population dynamics, this possibility remains largely unexplored. Here we model the spread of an allele encoding female mate preference for uninfected males alongside the spread of CI inducing Wolbachia. Mate preferences can evolve but the spread of the preference allele depends on factors associated with both Wolbachia infection and the preference allele itself. Incomplete maternal transmission of Wolbachia, fitness costs and low CI, improve the spread of the preference allele and impact on the population dynamics of Wolbachia. In addition, mate preferences are found in infected individuals. These results have important consequences for the fate of Wolbachia and studies addressing mate preferences in infected populations.     

Simple DNA sequences in homologous flanking regions near immunoglobulin VH genes: a role in gene interaction?

Five closely related immunoglobulin VH genes (subgroup II) were compared by sequencing of several kb of DNA. In three of the genes homology greater than 75% was found along an area of 4 kb that includes the coding region. The homology in flanking regions is only slightly lower than that in the coding sequences. Two other genes, which are located on the same EcoRI fragment, show high homology to the first three genes in the coding and immediately flanking regions. In more distant flanking regions no homology is found with the first three genes. This indicates that their evolutionary history differs from that of the other three genes. A region of simple DNA sequence composed of repetitive TCC and TCA elements was found at a distance of approximately 380 bp upstream from the initiator ATG of these VH genes. This region is the site where the two sets of genes abruptly start to diverge. The structure of the simple DNA sequence in the various VH genes suggests that it may be involved in gene interaction. We propose that both simple DNA sequences and homology in flanking regions serve a function in the correction of VH genes, which seem to be rather free to diverge and drift into pseudogenes. A correction mechanism may help this gene family to maintain its two major features, multiplicity and diversity.     

What can we learn from noncoding regions of similarity between genomes?

Background  

In addition to known protein-coding genes, large amounts of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome.     

Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins?

Intrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of IDPs. In spite of active research in past few decades, what induces structural disorder in IDPs and how is still elusive. Many studies testify that sequential and spatial neighbours often play important roles in determining structural and functional behaviour of proteins. Considering this fact, we assessed sequence neighbours of intrinsically disordered regions (IDRs) to understand if they have any role to play in inducing structural flexibility in IDPs. Our analysis includes 97% eukaryotic IDPs and 3% from bacteria and viruses. Physicochemical and structural parameters including amino acid propensity, hydrophobicity, secondary structure propensity, relative solvent accessibility, B-factor and atomic packing density are used to characterise the neighbouring residues of IDRs (NRIs). We show that NRIs exhibit a unique nature, which makes them stand out from both ordered and disordered residues. They show correlative occurrences of residue pairs like Ser-Thr and Gln-Asn, indicating their tendency to avoid strong biases of order or disorder promoting amino acids. We also find differential preferences of amino acids between N- and C-terminal neighbours, which might indicate a plausible directional effect on the dynamics of adjacent IDRs. We designed an efficient prediction tool using Random Forest to distinguish the NRIs from the ordered residues. Our findings will contribute to understand the behaviour of IDPs, and may provide potential lead in deciphering the role of IDRs in protein folding and assembly.     

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein–DNA system

N¹-meA and N³-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of S_N2 type methylating agents. We report here the structural characterization of these base lesions in duplex DNA using a cross-linked protein–DNA crystallization system. The crystal structure of N¹-meA:T pair shows an unambiguous Hoogsteen base pair with a syn conformation adopted by N¹-meA, which exhibits significant changes in the opening, roll and twist angles as compared to the normal A:T base pair. Unlike N¹-meA, N³-meC does not establish any interaction with the opposite G, but remains partially intrahelical. Also, structurally characterized is the N⁶-meA base modification that forms a normal base pair with the opposite T in duplex DNA. Structural characterization of these base methylation modifications provides molecular level information on how they affect the overall structure of duplex DNA. In addition, the base pairs containing N¹-meA or N³-meC do not share any specific characteristic properties except that both lesions create thermodynamically unstable regions in a duplex DNA, a property that may be explored by the repair proteins to locate these lesions.     

Can copper binding to the prion protein generate a misfolded form of the protein?

The native prion protein (PrP) has a two domain structure, with a globular folded α-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu²⁺ via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in β-sheet content. Cu²⁺ bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu⁺ can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu²⁺ binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized β-sheet structure, allowing us to suggest a potential mechanism for the initiation of β-sheet misfolding in the C-terminal domain by Cu²⁺.

Love or fear: Can punishment promote cooperation?

Cooperation is a paradox: Why should one perform a costly behavior only to increase the fitness of another? Human societies, in which individuals cooperate with genetically unrelated individuals on a considerably larger scale than most mammals do, are especially puzzling in this regard. Recently, the threat of punishment has been given substantial attention as one of the mechanisms that could help sustain human cooperation in such situations. Nevertheless, using punishment to explain cooperation only leads to further questions: Why spend precious resources to penalize free‐riders, especially if others can avoid this investment and cheaters can punish you back? Here, it is argued that current evidence supports punishment as an efficient means for the maintenance of cooperation, and that the gravity of proposed limitations of punishment for maintaining cooperation may have been overestimated in previous studies due to the features of experimental design. Most notably, the importance of factors as characteristic of human societies as reputation and language has been greatly neglected. Ironically, it was largely the combination of the two that enabled humans to shape costly punishment into numerous low‐cost and less detrimental strategies that clearly can promote human cooperation.     

Can estrogens promote hypertension during systemic lupus erythematosus?

SLE is a chronic autoimmune inflammatory disorder that predominantly affects young women. Based on this observation, it has been speculated that sex steroids, particularly estrogens, contribute to SLE disease progression. Young women with SLE are at an increased risk for the development of hypertension yet the reasons for this are unclear. One potential mechanism for the increased risk of hypertension during SLE is the chronic inflammation caused by immune complex mediated tissue injury. Estrogens are known to have an immunomodulatory role that can lead to the production of characteristic autoantibodies important for immune complex formation. Therefore, it is conceivable that during SLE estrogens contribute to tissue injury, increased inflammation and hypertension. This brief review discusses the increased risk for hypertension during SLE, the role of estrogens in immune system function, evidence for estrogens in SLE, and a possible link between estrogens and SLE hypertension.     

Can invasive Burmese pythons inhabit temperate regions of the southeastern United States?

Understanding potential for range expansion is critical when evaluating the risk posed by invasive species. Burmese pythons (Python molurus bivittatus) are established in southern Florida and pose a significant threat to native ecosystems. Recent studies indicate that climate suitable for the species P. molurus exists throughout much of the southern United States. We examined survivorship, thermal biology, and behavior of Burmese pythons from South Florida in a semi-natural enclosure in South Carolina, where winters are appreciably cooler than in Florida, but within the predicted region of suitable climate. All pythons acclimated to the enclosure, but most died after failing to seek appropriate refugia during sub-freezing weather. The remaining snakes used refugia but died during an unusually cold period in January 2010. Although all snakes died during the study, most survived extended periods at temperatures below those typical of southern Florida and none exhibited obvious signs of disease. Our study represents a first step in evaluating the results of climate matching models and we address factors that may affect range expansion in this invasive species.     

Interactions between prion protein isoforms: the kiss of death?

Direct interactions between the normal and aberrant forms of prion protein appear to be crucial in the transmission and pathogenesis of transmissible spongiform encephalopathies (TSEs) or prion diseases. Recent studies of such interactions in vitro have provided mechanistic insight into how TSE-associated prion protein might promote its own propagation in a manner that is specific enough to account, at least in part, for TSE strains and species barriers.     

Can correct protein models be identified?

The ability to separate correct models of protein structures from less correct models is of the greatest importance for protein structure prediction methods. Several studies have examined the ability of different types of energy function to detect the native, or native-like, protein structure from a large set of decoys. In contrast to earlier studies, we examine here the ability to detect models that only show limited structural similarity to the native structure. These correct models are defined by the existence of a fragment that shows significant similarity between this model and the native structure. It has been shown that the existence of such fragments is useful for comparing the performance between different fold recognition methods and that this performance correlates well with performance in fold recognition. We have developed ProQ, a neural-network-based method to predict the quality of a protein model that extracts structural features, such as frequency of atom-atom contacts, and predicts the quality of a model, as measured either by LGscore or MaxSub. We show that ProQ performs at least as well as other measures when identifying the native structure and is better at the detection of correct models. This performance is maintained over several different test sets. ProQ can also be combined with the Pcons fold recognition predictor (Pmodeller) to increase its performance, with the main advantage being the elimination of a few high-scoring incorrect models. Pmodeller was successful in CASP5 and results from the latest LiveBench, LiveBench-6, indicating that Pmodeller has a higher specificity than Pcons alone.     

How do ALS-associated mutations in superoxide dismutase 1 promote aggregation of the protein?

More than 100 different mutations in the gene encoding copper-zinc superoxide dismutase (SOD1) cause familial forms of amyotrophic lateral sclerosis (ALS)--a fatal neurodegenerative disease in which aggregation of the SOD1 protein is considered to be the primary mode of pathogenesis. Recent results show that these mutations have remarkably diverse and unexpected effects on the structure, activity and native state stability of SOD1. Intriguingly, many mutations seem to have no measurable effect on the biophysical and biochemical properties of SOD1, except for decreasing the net charge of the protein. Thus, it seems likely that different ALS-associated mutations promote SOD1 aggregation by fundamentally distinct mechanisms. Understanding this complexity has implications for drug development and treatment of the disease.     

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events.     

Can the fluorescence of green fluorescent protein chromophore be related directly to the nativity of protein structure?

In studies of green fluorescence protein (GFP) or other proteins with the use of GFP as a marker, the fluorescence of GFP is for the most part related directly to the nativity of its structure. Naturally, such a relation does exist since the chromophore of this protein is formed autocatalytically only just after GFP acquires its native structure. However, the fluorescence method may not yield reliable information on protein structure when studying renaturation and denaturation of this protein (with the formed chromophore). Using proteolysis, denaturant gradient gel electrophoresis and circular dichroism, we demonstrate herein that at major disturbances of the native structure of protein GFP-cycle3 the intensity of fluorescence of its chromophore can change insignificantly. In other words, the chromophore fluorescence does not reliably mirror alterations in protein structure. Since the main conclusions of this study are especially qualitative, it can be suggested that during renaturation/denaturation of wild-type GFP and its “multicolored” mutants their fluorescence is also not always associated with the changes in the structure of these proteins.