Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction

Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein–partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein–partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.     

Structural aspects of nucleic acid-sensing Toll-like receptors

Invading pathogens elicit potent immune responses in cells through interactions between structurally conserved molecules derived from the pathogens and specialized innate immune receptors such as the Toll-like receptors (TLRs). Nucleic acid is one of the principal TLR ligands. Nucleic acid-sensing TLRs recognize an array of nucleic acids, including double-stranded RNA, single-stranded RNA, and DNAs with specific sequence motifs. Although ligand-induced dimerization is commonly observed followed by TLR activation, both the specific recognition mechanisms and the ligand–receptor interactions vary among different TLRs. In this review, we highlight our current understanding of how these receptors recognize their cognate ligands based on the recent advances in structural biology.     

Theoretical study of electron transfer process between fullerenes and neurotransmitters; acetylcholine,dopamine, serotonin and epinephrine in nanostructures [neurotransmitters].C<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> complexes

Neurotransmitters are the compounds which allow the transmission of signals from one neuron to the next across synapses. They are the brain chemicals that communicate information throughout brain and body. Fullerenes are a family of carbonallotropes, molecules composed entirely of carbon, that take the forms of spheres, ellipsoids, and cylinders. Various empty carbon fullerenes (C_n) with different carbon atoms have been obtained and investigated. Topological indices have been successfully used to construct effective and useful mathematical methods to establish clear relationships between structural data and the physical properties of these materials. In this study, the number of carbon atoms in the fullerenes was used as an index to establish a relationship between the structures of neurotransmitters (NTs) acetylcholine (AC) 1, dopamine (DP) 2, serotonin (SE) 3, and epinephrine (EP) 4 as the well-known redox systems and fullerenes C_n (n = 60, 70, 76, 82, and 86) which create [NT].C_n; A-1 to A-5 up to D-1 to D-5. The relationship between the number of carbon atoms and the free energy of electron transfer (ΔG_et(n); n = 1–4) is assessed using the Rehm-Weller equation for A-1 to A-5 up to D-1 to D-5 supramolecular [NT].C_n complexes. The calculations are presented for the four reduction potentials (^Red.E₁ to ^Red.E₄) of fullerenes C_n. The results were used to calculate the four free energy values of electron transfer (ΔG_et(1) to ΔG_et(4)) of the supramolecular complexes A-1 to A-8 up to D-1 to D-8 for fullerenes C₆₀ to C₁₂₀. The first to fourth free activation energy values of electron transfer and the maximum wavelength of the electron transfers, ΔG^#_et(n) and λ_et (n = 1–4), respectively, were also calculated in this study for A-1 to A-8 up to D-1 to D-8 in accordance with the Marcus theory.     

Evolutionary food web models: effects of an additional resource

Many empirical food webs contain multiple resources, which can lead to the emergence of sub-communities—partitions—in a food web that are weakly connected with each other. These partitions interact and affect the complete food web. However, the fact that food webs can contain multiple resources is often neglected when describing food web assembly theoretically, by considering only a single resource. We present an allometric, evolutionary food web model and include two resources of different sizes. Simulations show that an additional resource can lead to the emergence of partitions, i.e. groups of species that specialise on different resources. For certain arrangements of these partitions, the interactions between them alter the food web properties. First, these interactions increase the variety of emerging network structures, since hierarchical bodysize relationships are weakened. Therefore, they could play an important role in explaining the variety of food web structures that is observed in empirical data. Second, interacting partitions can destabilise the population dynamics by introducing indirect interactions with a certain strength between predator and prey species, leading to biomass oscillations and evolutionary intermittence.     

Coffee volatiles induced after mechanical injury and beetle herbivory attract the coffee berry borer and two of its parasitoids

The coffee berry borer (CBB), Hypothenemus hampei (Ferrari), is the most important insect pest of coffee worldwide. In this study, we used headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry to sample and identify volatile compounds from Robusta coffee berries, Coffea canephora Pierre ex Froehner, infested with CBB and with mechanical damage. Furthermore, we evaluated the behavioral responses of the CBB and two of its parasitoids, Prorops nasuta Waterstone and Phymastichus coffea LaSalle, to three selected coffee volatile compounds in a Y-tube olfactometer. We found in the effluvia of red coffee berry compounds not previously reported for this coffee species. Our results show that Robusta coffee berries release induced volatiles either by insect herbivory or by mechanical damage. Small amount of butyl acetate, unknown compound 2, α-longipinene, longiborneol and longiborneol acetate are produced only in infested coffee berries fruits. Quantitatively, nine compounds account for the difference between healthy berries, infested, or mechanically damaged berries. Trans-ocimene, 4,8-dimethyl-3,7-nonadien-2-ol, α-copaene and kaurene increased amount levels in infested berries, while amount of methyl salicylate and linalool increased in mechanically damaged coffee berries. The olfactometric bioassays showed that CBB females and its two parasitoids were attracted to methyl salicylate. In addition, H. hampei and P. nasuta were attracted to linalool, and P. nasuta and P. coffea were attracted to trans-ocimene.     

Potential for oilseed rape resistance in pollen beetle control

Breeding for plant resistance to insect pests is a classic strategy in integrated management, but it has never been developed for use against European pests of oilseed rape (Brassica napus) (OSR), especially one of the most damaging ones, the pollen beetle (Meligethes aeneus). In this paper we look at the three strategies that could be employed to improve OSR resistance (based on transgenes, relatives of B. napus or OSR natural variation) and review our current knowledge as to how these strategies could be put into practice. We identify the drawbacks which are specific to the pollen beetle that could impede breeding programs for resistance, and propose an approach to circumvent them. Finally, we detail the steps of the interaction between OSR and the pollen beetle that could be targeted in order to improve plant resistance (host plant location, adult survival, adult feeding, egg production and oviposition, larval development) and discuss their efficiency and durability potential.