Grid-based state space exploration for molecular binding

Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is heavily limited by state space dimensionality. Here, we make the first steps towards a low-dimensional grid-based model of molecular binding. We discretise the state space of relative positions and orientations of the two molecules under the rigid body assumption.The corresponding program is published as the Python package molgri. For the rotational component of the grids, we test algorithms based on Euler angles, polyhedra and quaternions, of which the polyhedra-based are the most uniform. The program outputs a sequence of molecular structures that can be easily processed by standard MD programs to calculate grid point energies. We demonstrate the grid-based approach on two molecular systems: a water dimer and a coiled-coil protein interacting with a chloride anion. For the second system we relax the rigid-body assumption and improve the accuracy of the grid point energies by an energy minimisation. In both cases, oriented bonding patterns and energies confirm expectations from chemical intuition and MD simulations. We also demonstrate how analysis of energy contributions on a grid can be performed and demonstrate that electrostatically-driven association is sufficiently resolved by point-energy calculations. Overall, grid-based models of molecular binding are potentially a powerful complement to molecular sampling approaches, and we see the potential to expand the method to quantum chemistry and flexible docking applications.Comment: 13 pages, 7 figure

How Chromophore Labels Shape the Structure and Dynamics of a Peptide Hydrogel

Biocompatible and functionalizable hydrogels have a wide range of (potential) medicinal applications. The hydrogelation process, particularly for systems with very low polymer weight percentages (<1 wt %), remains poorly understood, making it challenging to predict the self-assembly of a given molecular building block into a hydrogel. This severely hinders the rational design of self-assembled hydrogels. In this study, we demonstrate the impact of an N-terminal group on the self-assembly and rheology of the peptide hydrogel hFF03 (hydrogelating, fibril forming peptide 03) using molecular dynamics simulations, oscillatory shear rheology, and circular dichroism spectroscopy. We find that the chromophore and even its specific regioisomers have a significant influence on the microscopic structure and dynamics of the self-assembled fibril, and on the macroscopic mechanical properties. This is because the chromophore influences the possible salt bridges, which form and stabilize the fibril formation. Furthermore, we find that the solvation shell fibrils by itself cannot explain the viscoelasticity of hFF03 hydrogels. Our atomistic model of the hFF03 fibril formation enables a more rational design of these hydrogels. In particular, altering the N-terminal chromophore emerges as a design strategy to tune the mechanic properties of these self-assembled peptide hydrogels

How chromophore labels shape the structure and dynamics of a peptide hydrogel

Biocompatible and functionalizable hydrogels have a wide range of (potential) medicinal applications. In contrast to conventional hydrogels formed by interconnected or interlocked polymer chains, self-assembled hydrogels form from small building blocks like short peptide chains. This has the advantage that the building blocks can be functionalized separately and then mixed to obtain the desired properties. However, the hydrogelation process for these systems, especially those with very low polymer weight percentage (< 1 wt%), is not well understood, and therefore it is hard to predict whether a given molecular building block will self-assemble into a hydrogel. This severely hinders the rational design of self-assembled hydrogels. In this study, we demonstrate the impact of an N-terminal chromophore label amino-benzoic acid on the self-assembly and rheology of hydrogel hFF03 (hydrogelating, fibril forming) using molecular dynamics simulations, which self-assembles into {\alpha}-helical coiled-coils. We find that the chromophore and even its specific regioisomers have a significant influence on the microscopic structure and dynamics of the self-assembled fibril, and on the macroscopic mechanical properties. This is because the chromophore influences the possible salt-bridges which form and stabilize the fibril formation. Furthermore we find that the solvation shell fibrils by itself cannot explain the viscoelasticity of hFF03 hydrogels. Our atomistic model of the hFF03 fibril formation enables a more rational design of these hydrogels. In particular, altering the N-terminal chromophore emergesas a design strategy to tune the mechanic properties of these self-assembled peptide hydrogels.Comment: 15 pages, 15 including appendi

Impact of glycan nature on structure and viscoelastic properties of glycopeptide hydrogels

Mucus is a complex biological hydrogel that acts as a barrier for almost everything entering or exiting the body. It is therefore of emerging interest for biomedical and pharmaceutical applications. Besides water, the most abundant components are the large and densely glycosylated mucins, glycoproteins of up to 20 MDa and carbohydrate content of up to 80 wt%. Here, we designed and explored a library of glycosylated peptides to deconstruct the complexity of mucus. Using the well-characterized hFF03 coiled-coil system as a hydrogel-forming peptide scaffold, we systematically probed the contribution of single glycans to the secondary structure as well as the formation and viscoelastic properties of the resulting hydrogels. We show that glycan-decoration does not affect α-helix and coiled-coil formation while it alters gel stiffness. By using oscillatory macrorheology, dynamic light scattering microrheology, and fluorescence lifetime-based nanorheology, we characterized the glycopeptide materials over several length scales. Molecular simulations revealed that the glycosylated linker may extend into the solvent, but more frequently interacts with the peptide, thereby likely modifying the stability of the self-assembled fibers. This systematic study highlights the interplay between glycan structure and hydrogel properties and may guide the development of synthetic mucus mimetics

Response of cattle with clinical osteochondrosis to mineral supplementation

Since 1982, farmers in the North West province and other parts of South Africa have noticed an increase in the incidence of lameness in cattle. Macro- and microscopical lesions of joints resembled osteochondrosis. Pre-trial data indicated that cattle with osteochondrotic lesions recovered almost completely when fed a supplement containing bio-available micro- and macrominerals of high quality. In the present trial, 43 clinically affected cattle of varying ages (1–5 years) and sexes were randomly divided into three groups. Each group was fed the same commercial supplement base with differing micro- and macromineral concentrations to determine the effect of mineral concentrations on the recovery from osteochondrosis. Both supplements 1 and 2 contained 25% of the recommended National Research Council (NRC) mineral values. Additional phosphate was added to supplement 2. Supplement 3, containing 80% of the NRC mineral values, was used as the control. Results from all three groups indicated no recovery from osteochondrosis. Urine pH of a small sample of the test cattle showed aciduria (pH < 6). Supplement analysis revealed addition of ammonium sulphate that contributed sulphate and nitrogen to the supplement. Supplementary dietary cation anion difference (DCAD) values were negative at -411 mEq/kg, -466 mEq/kg and -467 mEq/kg for supplements 1, 2 and 3, respectively, whereas the pre-trial supplement was calculated at +19.87 mEq/kg. It was hypothesised that feeding a low (negative) DCAD diet will predispose growing cattle to the development of osteochondrosis or exacerbate subclinical or clinical osteochondrosis in cattle.http://www.ojvr.orgam2017Paraclinical SciencesProduction Animal Studie

UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates.

The continuing emergence of SARS-CoV-2 variants calls for regular assessment to identify differences in viral replication, shedding and associated disease. In this study, African green monkeys were infected intranasally with either a contemporary D614G or the UK B.1.1.7 variant. Both variants caused mild respiratory disease with no significant differences in clinical presentation. Significantly higher levels of viral RNA and infectious virus were found in upper and lower respiratory tract samples and tissues from B.1.1.7 infected animals. Interestingly, D614G infected animals showed significantly higher levels of viral RNA and infectious virus in rectal swabs and gastrointestinal tract tissues. Our results indicate that B.1.1.7 infection in African green monkeys is associated with increased respiratory replication and shedding but no disease enhancement similar to human B.1.1.7 cases. ONE-SENTENCE SUMMARY: UK B.1.1.7 infection of African green monkeys exhibits increased respiratory replication and shedding but no disease enhancement

Resonance assignment and secondary structure of the middle MA-3 domain and complete tandem MA-3 region of the tumour suppressor protein Pdcd4

Pdcd4 (Programmed Cell Death Protein 4) is a novel eukaryotic tumour suppressor protein, which is involved in the regulation of both transcription and translation (reviewed in Lankat-Buttgereit and Göke 2009). The protein contains two interacting MA-3 domains (MA-3M and MA-3C), which are linked by a short semi-flexible linker region (Waters et al. 2007; Suzuki et al. 2008). The MA-3 domains are involved in mediating specific protein–protein interactions with functional partners such as eIF4A (Yang et al. 2003). Here we report essentially complete backbone and side chain 15N, 13C and 1H assignments for a construct composed of the middle MA-3 domain and subsequent linker region (MA-3M) and backbone assignments for the entire tandem MA-3 region of Pdcd4 (Pdcd4 MA-3M-C). Analysis of the backbone chemical shift data obtained indicates that Pdcd4 MA-3M contains eight helical regions corresponding to over 74% of the protein backbone and that Pdcd4 MA-3M-C contains fifteen helical regions (72%). Comparison of the position of these helical regions with those observed in the crystal structures suggests that the solution and crystal structures of both proteins are very similar

Acetylcholine receptors (muscarinic) (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

Muscarinic acetylcholine receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on Muscarinic Acetylcholine Receptors [45]) are GPCRs of the Class A, rhodopsin-like family where the endogenous agonist is acetylcholine. In addition to the agents listed in the table, AC-42, its structural analogues AC-260584 and 77-LH-28-1, N-desmethylclozapine, TBPB and LuAE51090 have been described as functionally selective agonists of the M1 receptor subtype via binding in a mode distinct from that utilized by non-selective agonists [243, 242, 253, 155, 154, 181, 137, 11, 230]. There are two pharmacologically characterised allosteric sites on muscarinic receptors, one defined by it binding gallamine, strychnine and brucine, and the other defined by the binding of KT 5720, WIN 62,577, WIN 51,708 and staurosporine [161, 162]

Microfabricated wire arrays for Z-pinch.

Microfabrication methods have been applied to the fabrication of wire arrays suitable for use in Z. Self-curling GaAs/AlGaAs supports were fabricated as an initial route to make small wire arrays (4mm diameter). A strain relief structure that could be integrated with the wire was designed to allow displacements of the anode/cathode connections in Z. Electroplated gold wire arrays with integrated anode/cathode bus connections were found to be sufficiently robust to allow direct handling. Platinum and copper plating processes were also investigated. A process to fabricate wire arrays on any substrate with wire thickness up to 35 microns was developed. Methods to handle and mount these arrays were developed. Fabrication of wire arrays of 20mm diameter was demonstrated, and the path to 40mm array fabrication is clear. With some final investment to show array mounting into Z hardware, the entire process to produce a microfabricated wire array will have been demonstrated