TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity.

SUMMARY: Comparisons of protein structures are critical for developing novel protein designs, annotating protein functions and predicting protein structure. The template modeling score (TM-score) is a widely used but computationally expensive measure of protein similarity that is applicable to a wide variety of structural biology problems. We introduce TMQuery-a continuously updated database containing over eight billion pre-computed TM-score values for every pair of proteins in the Protein Data Bank, allowing researchers to quickly query and download TM-scores via a web interface. AVAILABILITY AND IMPLEMENTATION: Publicly available at https://tmquery.gsk.com/.

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation.

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces.

Remarkably low affinity of CD4/peptide-major histocompatibility complex class II protein interactions.

The αß T-cell coreceptor CD4 enhances immune responses more than 1 million-fold in some assays, and yet the affinity of CD4 for its ligand, peptide-major histocompatibility class II (pMHC II) on antigen-presenting cells, is so weak that it was previously unquantifiable. Here, we report that a soluble form of CD4 failed to bind detectably to pMHC II in surface plasmon resonance-based assays, establishing a new upper limit for the solution affinity at 2.5 mM. However, when presented multivalently on magnetic beads, soluble CD4 bound pMHC II-expressing B cells, confirming that it is active and allowing mapping of the native coreceptor binding site on pMHC II. Whereas binding was undetectable in solution, the affinity of the CD4/pMHC II interaction could be measured in 2D using CD4- and adhesion molecule-functionalized, supported lipid bilayers, yielding a 2D Kd of ∼5,000 molecules/µm(2) This value is two to three orders of magnitude higher than previously measured 2D Kd values for interacting leukocyte surface proteins. Calculations indicated, however, that CD4/pMHC II binding would increase rates of T-cell receptor (TCR) complex phosphorylation by threefold via the recruitment of Lck, with only a small, 2-20% increase in the effective affinity of the TCR for pMHC II. The affinity of CD4/pMHC II therefore seems to be set at a value that increases T-cell sensitivity by enhancing phosphorylation, without compromising ligand discrimination.

Recent Advances in Electrosynthesized Molecularly Imprinted Polymer Sensing Platforms for Bioanalyte Detection.

The accurate detection of biological materials has remained at the forefront of scientific research for decades. This includes the detection of molecules, proteins, and bacteria. Biomimetic sensors look to replicate the sensitive and selective mechanisms that are found in biological systems and incorporate these properties into functional sensing platforms. Molecularly imprinted polymers (MIPs) are synthetic receptors that can form high affinity binding sites complementary to the specific analyte of interest. They utilise the shape, size, and functionality to produce sensitive and selective recognition of target analytes. One route of synthesizing MIPs is through electropolymerization, utilising predominantly constant potential methods or cyclic voltammetry. This methodology allows for the formation of a polymer directly onto the surface of a transducer. The thickness, morphology, and topography of the films can be manipulated specifically for each template. Recently, numerous reviews have been published in the production and sensing applications of MIPs; however, there are few reports on the use of electrosynthesized MIPs (eMIPs). The number of publications and citations utilising eMIPs is increasing each year, with a review produced on the topic in 2012. This review will primarily focus on advancements from 2012 in the use of eMIPs in sensing platforms for the detection of biologically relevant materials, including the development of increased polymer layer dimensions for whole bacteria detection and the use of mixed monomer compositions to increase selectivity toward analytes.

The effect of topology on the structure and free energy landscape of DNA kissing complexes.

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0, or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.

N-Terminal speciation for native chemical ligation.

Native chemical ligation (NCL) enables the chemical synthesis of peptides via reactions between N-terminal thiolates and C-terminal thioesters under mild, aqueous conditions at pH 7-8. Here we demonstrate quantitatively how thiol speciation at N-terminal cysteines and analogues varies significantly depending upon structure at typical pH values used in NCL.

A soft photopolymer cuboid that computes with binary strings of white light.

Next-generation stimuli-responsive materials must be configured with local computational ability so that instead of a discrete on-off responsiveness, they sense, process and interact reciprocally with environmental stimuli. Because of their varied architectures and tunable responsiveness to a range of physical and chemical stimuli, polymers hold particular promise in the generation of such "materials that compute". Here, we present a photopolymer cuboid that autonomously performs pattern recognition and transfer, volumetric encoding and binary arithmetic with incandescent beams. The material's nonlinear response to incident beams generates one, two or three mutually orthogonal ensembles of white-light filaments, which respectively self-organize into disordered, 1-D and 2-D periodic geometries. Data input as binary (dark-bright) strings generate a unique distribution of filament geometries, which corresponds to the result of a specific operation. The working principles of this material that computes with light is transferrable to other nonlinear systems and incoherent sources including light emitting diodes.

Synthesis of Optimized Molecularly Imprinted Polymers for the Isolation and Detection of Antidepressants via HPLC.

Antidepressants such as amitryptiline and fluoxetine are on the list of modern essential medicines of the World Health Organization. However, there are growing concerns regarding the ecological impact of these pharmaceuticals, leading to a great need to improve current wastewater treatment procedures. In this contribution, we will report on the use of molecularly imprinted polymers (MIPs) for the extraction of antidepressants in water samples. MIPs were developed for fluoxetine and duloxetine, antidepressants belonging to the class of selective serotonin reuptake inhibitors (SSRIs). The binding capacity of these microparticles was evaluated using ultraviolet-visible (UV-Vis) spectroscopy. A new high-performance liquid chromatography (HPLC) procedure coupled to UV detection was developed, which enabled the study of mixtures of fluoxetine and duloxetine with other nitrogen-containing compounds. These results indicate that it is possible to selectively extract SSRIs from complex samples. Therefore, these versatile polymers are a promising analytical tool for the clean-up of water samples, which will benefit aquatic life and reduce the ecological impact of pharmaceuticals.

Heat-Transfer Method: A Thermal Analysis Technique for the Real-Time Monitoring of Staphylococcus aureus Growth in Buffered Solutions and Digestate Samples.

The identification and quantification of microorganisms in water samples are crucial to improve processes in organic waste treatment facilities. Most of the currently available tests are either labor intense or costly, and they do not allow determination of the dynamics within microbial communities in digestate samples. This study is the first report on the use of thermal analysis, specifically the heat transfer method (HTM), to monitor microbial load in aqueous systems and digestate samples. Staphylococcus aureus was used as a model organism, and different concentrations in water were measured by the HTM. It was demonstrated that there was a positive correlation between the thermal resistance and concentration of the bacterial cells. Subsequently, the influence of temperature on growth rates was studied and confirmed by plating experiments and scanning electron microscopy (SEM). These results showed the possibility to monitor the temperature-dependent growth of S. aureus using the HTM. To determine if this technique can be applied for studying complex matrices, digestate samples were collected from a number of sources and plated on nutrient agar plates. The bacterial cultures derived from single colonies were characterized and identified by sequencing of DNA regions for 16S rRNA. HTM measurements were performed in diluted or centrifuged digestate samples that were enriched with S. aureus. The results indicated that it is possible to evaluate microbial load even in samples containing other organic material. The thermal analysis method has the potential to provide a low-cost monitoring option, which is simple to use and provides real-time analysis, thus improving the existing monitoring procedures in organic waste treatment facilities.

Self-Organized Lattices of Nonlinear Optochemical Waves in Photopolymerizable Fluids: The Spontaneous Emergence of 3-D Order in a Weakly Correlated System.

Many of the extraordinary three-dimensional architectures that pattern our physical world emerge from complex nonlinear systems or dynamic populations whose individual constituents are only weakly correlated to each other. Shoals of fish, murmuration behaviors in birds, congestion patterns in traffic, and even networks of social conventions are examples of spontaneous pattern formation, which cannot be predicted from the properties of individual elements alone. Pattern formation at a different scale has been observed or predicted in weakly correlated systems including superconductors, atomic gases near Bose Einstein condensation, and incoherent optical fields. Understanding pattern formation in nonlinear weakly correlated systems, which are often unified through mathematical expression, could pave intelligent self-organizing pathways to functional materials, architectures, and computing technologies. However, it is experimentally difficult to directly visualize the nonlinear dynamics of pattern formation in most populations-especially in three dimensions. Here, we describe the collective behavior of large populations of nonlinear optochemical waves, which are poorly correlated in both space and time. The optochemical waves-microscopic filaments of white light entrapped within polymer channels-originate from the modulation instability of incandescent light traveling in photopolymerizable fluids. By tracing the three-dimensional distribution of optical intensity in the nascent polymerizing system, we find that populations of randomly distributed, optochemical waves synergistically and collectively shift in space to form highly ordered lattices of specific symmetries. These, to our knowledge, are the first three-dimensionally periodic structures to emerge from a system of weakly correlated waves. Their spontaneous formation in an incoherent and effectively chaotic field is counterintuitive, but the apparent contradiction of known behaviors of light including the laws of optical interference can be explained through the soliton-like interactions of optochemical waves with nearest neighbors. Critically, this work casts fundamentally new insight into the collective behaviors of poorly correlated nonlinear waves in higher dimensions and provides a rare, accessible platform for further experimental studies of these previously unexplored behaviors. Furthermore, it defines a self-organization paradigm that, unlike conventional counterparts, could generate polymer microstructures with symmetries spanning all the Bravais lattices.