Extracting atomic contributions to binding free energy from molecular dynamics simulations with mixed solvents (MDmix)

Background: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Method: Mixed solvents MD simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery Result: As such, they are hardly transferable to different molecules. Conclusion: To achieve transferable energies, we present here a method for decomposing the molecular binding free energy into accurate atomic contributions and we demonstrate with two qualitative visual examples how the corrected energy maps better match known binding hotspots and how they can reveal hidden hotspots with actual drug design potential.

Discrete LAT condensates encode antigen information from single pMHC:TCR binding events

LAT assembly into a two-dimensional protein condensate is a prominent feature of antigen discrimination by T cells. Here, we use single-molecule imaging techniques to resolve the spatial position and temporal duration of each pMHC:TCR molecular binding event while simultaneously monitoring LAT condensation at the membrane. An individual binding event is sufficient to trigger a LAT condensate, which is self-limiting, and neither its size nor lifetime is correlated with the duration of the originating pMHC:TCR binding event. Only the probability of the LAT condensate forming is related to the pMHC:TCR binding dwell time. LAT condenses abruptly, but after an extended delay from the originating binding event. A LAT mutation that facilitates phosphorylation at the PLC-γ1 recruitment site shortens the delay time to LAT condensation and alters T cell antigen specificity. These results identify a role for the LAT protein condensation phase transition in setting antigen discrimination thresholds in T cells.

Genetic Basis of Follicle Development in Dazu Black Goat by Whole-Transcriptome Sequencing

The follicle development (FD) is an important factor determining litter size in animals. Recent studies have found that noncoding RNAs (ncRNAs) play an important role in FD. In particular, the role of the regulatory mechanism of competing endogenous RNAs (ceRNAs) that drive FD has attracted increasing attention. Therefore, this study explored the genetic basis of goat FD by obtaining the complete follicular transcriptome of Dazu black goats at different developmental stages. Results revealed that 128 messenger RNAs (mRNAs), 4 long noncoding RNAs (lncRNAs), 49 microRNAs (miRNAs), and 290 circular RNAs (circRNAs) were significantly differentially expressed (DE) between large and small follicles. Moreover, DEmRNAs were enriched in many signaling pathways related to FD, as well as GO terms related to molecular binding and enzyme activity. Based on the analysis of the ceRNA network (CRN), 34 nodes (1 DElncRNAs, 10 DEcircRNAs, 14 DEmiRNAs, and 9 DEmRNAs) and 35 interactions (17 DEcircRNAs–DEmRNAs, 2 DElncRNAs–DEmiRNAs, and 16 DEmRNA–DEmiRNAs) implied that the CRN could be involved in the FD of goats. In conclusion, we described gene regulation by DERNAs and lncRNA/circRNA–miRNA–mRNA CRNs in the FD of goats. This study provided insights into the genetic basis of FD in precise transcriptional regulation.

Improving Small-Molecule Force Field Parameters in Ligand Binding Studies

Small molecules are major players of many chemical processes in diverse fields, from material science to biology. They are made by a combination of carbon and heteroatoms typically organized in system-specific structures of different complexity. This peculiarity hampers the application of standard force field parameters and their in silico study by means of atomistic simulations. Here, we combine quantum-mechanics and atomistic free-energy calculations to achieve an improved parametrization of the ligand torsion angles with respect to the state-of-the-art force fields in the paradigmatic molecular binding system benzamidine/trypsin. Funnel-Metadynamics calculations with the new parameters greatly reproduced the high-resolution crystallographic ligand binding mode and allowed a more accurate description of the binding mechanism, when the ligand might assume specific conformations to cross energy barriers. Our study impacts on future drug design investigations considering that the vast majority of marketed drugs are small-molecules.

Proteome Microarray Screening Identifies Human Polyphosphate-Binding Proteins in the Phosphatidylinositol Signaling Pathway

Polyphosphates are linear chains of orthophosphate residues that are present in all living cells. Polyphosphates are released from platelet d-granules and are also produced in bacteria. Polyphosphates are procoagulant in mammalian species and in bacteria are required for energy and phosphate storage, stress resistance, chelation of metal ions and escaping host immunity. Despite these pleiotropic effects, sparse information is available on molecular binding partners of polyphosphates. Here, we used a slide-based human proteome microarray screen for the search of polyphosphate-binding proteins. This approach suggested several novel proteins with relation to the phosphatidylinositol signaling pathway. The highest signals were obtained for Disabled-1 (DAB1) and phosphatidylinositol-5-phosphate 4-kinase 2B (PIP4K2B). Isothermal titration calorimetry was used for confirmation of DAB1 interactions with long-chain polyphosphates. These results offer new rationale to further investigate the interference of polyphosphates with intracellular signaling pathways.

Ecological memory preserves phage resistance mechanisms in bacteria

Bacterial defenses against phage, which include CRISPR-mediated immunity and other mechanisms, can carry substantial growth rate costs and can be rapidly lost when pathogens are eliminated. How bacteria preserve their molecular defenses despite their costs, in the face of variable pathogen levels and inter-strain competition, remains a major unsolved problem in evolutionary biology. Here, we present a multilevel model that incorporates biophysics of molecular binding, host-pathogen population dynamics, and ecological dynamics across a large number of independent territories. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of defenses, hosts sustain sufficient levels of pathogen within an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions, selects against cheater strains that avoid the costs of immunity, and enables co-evolutionary dynamics in a wide range of systems.

From Photon to Oganesson: Lie Algebra Realization of the Standard Model Extending over the Periodic Table

As reported in a series of previous PIRT conferences, a direct SU(3) structural realization of the Standard Model has been developed based upon Marius Sophus Lie’s original Norwegian Ph.D. thesis Over en Classe Geometriske Transformationer from 1871 (and thus due for a most deserved 150-year anniversary). It elucidates how “the theory of main tangential curves can be brought back to that of rounded curves”, anticipating a coherent linear representation of the elementary particles instead of the rotational chosen since they were considered point-like and amorphous when they many years later entered the stage. Under these premises the Standard Model has built a magnificent, undoubtedly true but congested multi-particle system whereas the Lie continuous transformation element, the partial derivative ’straight line of length equal to zero’ outlines an isotropic vector matrix lattice of crystallographic Killing root space diagram A3 form which from the Nucleon and inwards can backtrack the Standard Model geometrically, as well as continue outward iterating to a space-filling solid state R3×SO(3) wave-packet complex tessellating the whole periodic table with electron shells and subshells, isotope spectrum, neutron captures, radiative channels, oxidation states, molecular binding sites etc. in successive layers also including the Lanthanides in the sixth period and the Actinides in the seventh, in which now the concluding Oganesson has been reached in perfectly well-built saturated noble gas shape and condition.

Probing the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility

Clustering of ligand:receptor complexes on the cell membrane is widely presumed to have functional consequences for subsequent signal transduction. However, it is experimentally challenging to selectively manipulate receptor clustering without altering other biochemical aspects of the cellular system. Here, we develop a microfabrication strategy to produce substrates displaying mobile and immobile ligands that are separated by roughly 1 µm, and thus experience an identical cytoplasmic signaling state, enabling precision comparison of downstream signaling reactions. Applying this approach to characterize the ephrinA1:EphA2 signaling system reveals that EphA2 clustering enhances both receptor phosphorylation and downstream signaling activity. Single-molecule imaging clearly resolves increased molecular binding dwell times at EphA2 clusters for both Grb2:SOS and NCK:N-WASP signaling modules. This type of intracellular comparison enables a substantially higher degree of quantitative analysis than is possible when comparisons must be made between different cells and essentially eliminates the effects of cellular response to ligand manipulation.

Synthesis and Application of Fish Gelatin for Hydrogels/ Composite Hydrogels: A Review

Hydrogels are one of the biopolymers that have been applied and have excellent potential to be developed as a raw material in future food technology, biomedicine, and three-dimensional (3D) bioprinting. Even stigmatized that hydrogels are the only source of bioink for 3D bioprinting. Among natural sources, protein-based hydrogels have advantages in the aspects of biocompatibility, biodegradability, tunability, molecular binding ability, and bioactive properties. Gelatin is a natural protein-based biopolymer that offers potential. Besides its advantages as a natural protein-based hydrogel, gelatin is also inexpensive, usually extracted from processing by-products such as skins and bones. Studies also mentioned that gelatin has the tripeptide motif that promotes cell attachment for subsequent cellular processes, like migration, differentiation, and proliferation. However, most gelatin is derived from mammalian sources, while these sources are limited considering socio-religion, cultural, health aspects. Fish gelatin is the most potential source for alternative gelatin. They have uniqueness and viscosity for bio-fabrication and injectable hydrogels. Therefore, this paper will review the hydrogels based on fish gelatin studied in recent years and the last decade. Here also described the stages in the fabrication of fish gelatin hydrogels/hydrogel composites with different co-polymers, composite materials, polymerization methods, and future intended use of obtained fish gelatin hydrogels/composites.

INDI - Integrated Nanobody Database for Immunoinformatics

Nanobodies, a subclass of antibodies found in camelids, are a versatile molecular binding scaffold composed of a single polypeptide chain. The small size of nanobodies bestows multiple therapeutic advantages (stability, tumor penetration) with the first therapeutic approval in 2018 cementing the clinical viability of this format. Structured data and sequence information of nanobodies will enable the accelerated clinical development of nanobody-based therapeutics. Though the nanobody sequence and structure data are deposited in the public domain at an accelerating pace, the heterogeneity of sources and lack of standardization hampers reliable harvesting of nanobody information. We address this issue by creating the Integrated Database of Nanobodies for Immunoinformatics (INDI, http://research.naturalantibody.com/nanobodies). INDI collates nanobodies from all the major public outlets of biological sequences: patents, GenBank, next-generation sequencing repositories, structures and scientific publications. We equip INDI with powerful nanobody-specific sequence and text search facilitating access to more than 11 million nanobody sequences. INDI should facilitate development of novel nanobody-specific computational protocols helping to deliver on the therapeutic promise of this drug format.