Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields.

Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields. We also evaluate the relative stabilities of the three main interfaces present in the icosahedral capsid using locally restricted docking with Rosetta. Both the rescoring and locally restricted docking results report a particularly stable protein-protein interface, which is the most likely intermediate during the first stage of the hierarchical capsid assembly. The blind docking results rescored with both Amber and Rosetta yield docking funnels, i.e., three or more near-native structures among the top five predictions. The results support experimental observations on in vitro assembly of CCMV capsids. The cross-validation of the results suggests that energy-landscape-based methods with biomolecular force fields have the potential to improve existing docking procedures.

Design of a Kagome lattice from soft anisotropic particles.

We present a simple model of triblock Janus particles based on discoidal building blocks, which can form energetically stabilized Kagome structures. We find 'magic number' global minima in small clusters whenever particle numbers are compatible with a perfect Kagome structure, without constraining the accessible three-dimensional configuration space. The preference for planar structures with two bonds per patch among all other possible minima on the landscape is enhanced when sedimentation forces are included. For the building blocks in question, structures containing three bonds per patch become progressively higher in energy compared to Kagome structures as sedimentation forces increase. Rearrangements between competing structures, as well as ring formation mechanisms are characterised and found to be highly cooperative.

Global optimization of cholic acid aggregates.

In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.

Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.

Intermediates of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales either by studying oligomers in equilibrium or by focusing on their dissociation instead of their association. Our previous studies showed that among the three possible dimer interfaces in the icosahedral capsid, two are thermodynamically relevant for capsid formation. The aim of the current study is to evaluate the relative structural stabilities of the three different ss-CCMV dimers and to find and understand the conditions that lead to their dissociation. Long timescale molecular dynamics simulations at 300 K of the various dimers and of the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. Simulations in implicit solvent show that at higher temperature (350 K), the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable interface. The pentamer of dimers is also found to be stable on long timescales at 300 K, with an inherent flexibility of the outer protein chains.

Design of self-assembling mesoscopic Goldberg polyhedra.

Palladium ions complexed with nonlinear bidentate ligands have been shown to form hollow, spherical shells with high symmetries. We show that such structures can be reproduced using model anisotropic mesoscale building blocks featuring excluded volume and long-range ionic interactions. A linear building block with a central charged particle, in combination with a bent 'ligand' particle with opposite charges at the ends is sufficient to drive the system towards planar coordination, and the charge ratio determines the coordination number. Similar to the molecular systems, the bend in the 'ligand' particle determines the curvature of the shells that these building blocks prefer. Besides reproducing exotic structures such as M30L60 and M48L96 tetravalent Goldberg polyhedra, we identify highly cooperative single transition state rearrangements between low-energy competing structures as well, corresponding to rotatory motions of a planar subunit within the spherical shell.

Longitudinal determination of BNT162b2 vaccine induced strongly binding SARS-CoV-2 IgG antibodies in a cohort of Romanian healthcare workers.

Mass vaccination against the disease caused by the novel coronavirus (COVID-19) was a crucial step in slowing the spread of SARS-CoV-2 in 2021. Even in the face of new variants, it still remains extremely important for reducing hospitalizations and COVID-19 deaths. In order to better understand the short- and long-term dynamics of humoral immune response, we present a longitudinal analysis of post-vaccination IgG levels in a cohort of 166 Romanian healthcare workers vaccinated with BNT162b2 with weekly follow-up until 35 days past the first dose and monthly follow-up up to 6 months post-vaccination. A subset of the patients continued with follow-up after 6 months and either received a booster dose or got infected during the Delta wave in Romania. Tests were carried out on 1694 samples using a CE-marked IgG ELISA assay developed in-house, containing S1 and N antigens of the wild type virus. Participants infected with SARS-CoV-2 before vaccination mount a quick immune response, reaching peak IgG levels two weeks after the first dose, while IgG levels of previously uninfected participants mount gradually, increasing abruptly after the second dose. Overall higher IgG levels are maintained for the previously infected group throughout the six month primary observation period (e.g. 36-65 days after the first dose, the median value in the previously infected group is 5.29 AU/ml, versus 3.58 AU/ml in the infection naïve group, p less than 0.001). The decrease of IgG levels is gradual, with lower median values in the infection naïve cohort even 7-8 months after vaccination, compared to the previously infected cohort (0.7 AU/ml versus 1.29 AU/ml, p = 0.006). Administration of a booster dose yielded higher median IgG antibody levels than post second dose in the infection naïve group and comparable levels in the previously infected group.

Spectroscopic studies on photodegradation of atorvastatin calcium.

In this work, the photodegradation process of atorvastatin calcium (ATC) is reported as depending on: (1) the presence and the absence of excipients in the solid state; (2) the chemical interaction of ATC with phosphate buffer (PB) having pH equal to 7 and 8; and (3) hydrolysis reaction of ATC in the presence of aqueous solution of NaOH. The novelty of this work consists in the monitoring of the ATC photodegradation by photoluminescence (PL). The exposure of ATC in solid state to UV light induces the photo-oxygenation reactions in the presence of water vapors and oxygen from air. According to the X-ray photoelectron spectroscopic studies, we demonstrate that the photo-oxygenation reaction leads to photodegradation compounds having a high share of C=O bonds compared to ATC before exposure to UV light. Both in the presence of PB and NaOH, the photodegradation process of ATC is highlighted by a significant decrease in the intensity of the PL and photoluminescence excitation (PLE) spectra. According to PLE spectra, the exposure of ATC in the presence of NaOH to UV light leads to the appearance of a new band in the spectral range 340-370 nm, this belonging to the photodegradation products. Arguments concerning the chemical compounds, that resulted in this last case, are shown by Raman scattering and FTIR spectroscopy.

Extremely rare "daisy-like" crystals in urinary sediment can be due to a sampling artifact.

Manual urine sediment analysis of a sample obtained from a 5 year old child by our clinical diagnostics laboratory revealed abundant "daisy-like" crystals, which have been first described in 2004 and found to be extremely rare in a follow-up publication by the same research group. To date only 12 samples have been described in the literature containing such crystals. Upon further investigation on how the sample was obtained, we were able to reproduce the process without any biological specimen involved. We show that these crystals are in fact contaminants from the sample collection recipient itself, which was a glass recipient sterilized by the patient's family the night before sample collection, by boiling water with high calcium and magnesium content (hard water), and letting the recipient cool overnight with the water in it. The obtained abundant "daisy-like" crystals readily dissolve in acidic environment, and are composed most likely of mostly calcium carbonate. Sampling artifacts are therefore a possible explanation for at least some of the previously described "daisy-like" urinary crystals, as the formation of such crystals does not need to involve any biomolecules, only hard water and appropriate crystallization conditions for the limescale in it.

Symmetrization of the AMBER and CHARMM force fields.

The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization.

Interpolation schemes for peptide rearrangements.

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

Minimalistic coarse-grained modeling of viral capsid assembly.

The spontaneous formation of virus capsids from multiple copies of capsid proteins is a fascinating example of supramolecular self-assembling processes. Most known viruses protect their genome with icosahedral capsids, but other morphologies exist as well, including elongated, conical, tubular, head-tail structures. The mechanisms of assembly can be diverse and are still not perfectly understood. In this chapter we present theoretical models developed over the years that reproduce the basic physics of self-assembly of empty viral capsids. All these models are highly coarse-grained, as it is still not possible to access the long timescales of such processes with atomistic modeling. Very different particle-based models can result in the same overall behavior, showing that such processes are governed by the effective anisotropic interactions between protein building blocks.

Reusable on-plate immunoprecipitation method with covalently immobilized antibodies on a protein G covered microtiter plate.

Covalent immobilization of antibodies to protein G beads is a basic molecular biology method, although the beads present poor recovery results. Our aim was to reuse the immobilized antibody-protein G complex on a very small scale, therefore we optimized the crosslinking procedure to be used on the wells of a standard 96-well microplate. The method used involves the affinity binding of the antibody to the protein G surface, followed by the immobilization step using different crosslinking reagents, DMP and BS3, quenching the crosslinking reaction, and binding the antibody-specific antigen. By scaling down the procedure, we were able to reuse the anti-EGFR crosslinked wells more than 20 times. This method can be used to perform assays on a wide range of solid supports containing the protein G in an immobilized form, including functionalized nanosensors, for immunoprecipitation, protein and cell lysate purification, target protein enrichment.

Influence of Reduced Graphene Oxide on the Electropolymerization of 5-amino-1-naphthol and the Interaction of 1,4-phenylene Diisothiocyanate with the Poly(5-amino-1-naphtol)/Reduced Graphene Oxide Composite.

A new composite base on reduced graphene oxide (RGO) and poly(5-amino-1-naphthol) (P5A1N) was synthesized by the electrochemical polymerization of 5-amino-1-naphthol (5A1N) in the presence of HClO4 and H4SiW12O40 onto the surface of Au electrode covered with the RGO sheets. The linear dependence of the current densities of the anodic and cathodic peaks with the scan rate of the potential range (0; 0.8) V vs. SCE, reported during electropolymerization of 5A1N, indicates an electron transfer that is controlled by diffusion. A covalent functionalization of the RGO sheets with P5A1N is argued by: (i) the simultaneous disappearance of the IR band at 1584 cm-1 and the appearance of the new IR bands at 812, 976 and 3744 cm-1, and (ii) the appearance of two Raman lines at 738 and 1428 cm-1. An application of the RGO sheets covalently functionalized with P5A1N is demonstrated to support 1,4-phenylene diisothiocyanate (PDITC), a compound used as a cross-linking agent for various biological applications. The chemical adsorption of PDITC onto the RGO sheets covalently functionalized with P5A1N, which involves the appearance of new functional groups of the type thiourea, was proven by Raman scattering and IR spectroscopy.

Design principles for Bernal spirals and helices with tunable pitch.

Using the framework of potential energy landscape theory, we describe two in silico designs for self-assembling helical colloidal superstructures based upon dipolar dumbbells and Janus-type building blocks, respectively. Helical superstructures with controllable pitch length are obtained using external magnetic field driven assembly of asymmetric dumbbells involving screened electrostatic as well as magnetic dipolar interactions. The pitch of the helix is tuned by modulating the Debye screening length over an experimentally accessible range. The second design is based on building blocks composed of rigidly linked spheres with short-range anisotropic interactions, which are predicted to self-assemble into Bernal spirals. These spirals are quite flexible, and longer helices undergo rearrangements via cooperative, hinge-like moves, in agreement with experiment.

Local frustration determines molecular and macroscopic helix structures.

Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of ß strands in a bilayered extended ß-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids. The relative orientation of the ellipsoids dictates the morphology of the resulting assembly. Amyloid structures derived from experiment are consistent with our model, and we use magnets to demonstrate that the frustration principle is scale and system independent. In contrast to other models of amyloid, our model isolates the effect of frustration from the fundamental interactions between building blocks to reveal the frustration rather than dependence of morphology on the physical interactions. Consequently, amyloid is viewed as a discrete molecular version of the more general macroscopic frustrated bilayer that is exemplified by Bauhinia seedpods. The model supports the idea that the interactions arising from an arbitrary peptide sequence can support an amyloid structure if a bilayer can form first, which suggests that supplementary protein sequences, such as chaperones or decorative domains, could play a significant role in stabilizing such bilayers and therefore in selecting morphology during nucleation. Our model provides a foundation for exploring the effects of frustration on higher-order superstructural polymorphic assemblies that may exhibit complex functional behavior. Two outstanding examples are the systematic kinking of decorated fibers and the nested frustration of the Bauhinia seedpod.

Emergent complexity from simple anisotropic building blocks: shells, tubes, and spirals.

We describe a remarkably simple, generic, coarse-grained model involving anisotropic interactions, and characterize the global minima for clusters as a function of various parameters. Appropriate choices for the anisotropic interactions can reproduce a wide variety of complex morphologies as global minima, including spheroidal shells, tubular, helical and even head-tail morphologies, elucidating the physical principles that drive the assembly of these mesoscopic structures. Our model captures several experimental observations, such as the existence of competing morphologies, capsid polymorphism, and the effect of scaffolding proteins on capsid assembly.

Energy landscapes for shells assembled from pentagonal and hexagonal pyramids.

We present new rigid body potentials that should favour efficient self-assembly of pentagonal and hexagonal pyramids into icosahedral shells over a wide range of temperature. By adding an extra repulsive site opposite the existing apex sites of the pyramids considered in a previously published model, frustrated energy landscapes are transformed into systems identified with self-assembling properties. The extra interaction may be considered analogous to a hydrophobic-hydrophilic repulsion, as in micelle formation.

Helix self-assembly from anisotropic molecules.

We explore the potential energy landscape for clusters composed of disklike ellipsoidal particles interacting via an anisotropic potential based on the elliptic contact function. Over a wide range of parameter space we find global potential energy minima consisting of helices composed of one or more strands. Characterizing the potential energy surface in the region of helical global minima reveals a topology associated with "structure-seeking" systems. This result indicates that the helices will self-assemble over a wide range of temperature.

Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation.

A refined grid of a conformational potential energy surface (PES) and a conformational entropy surface for glycine diamide was generated by ab initio molecular computations. The possible network of reaction paths was recognized in terms of the linear combinations of internal coordinates corresponding to conrotatory and disrotatory modes of motions. Such a Woodward-Hoffmann-like path selection principle was detected for the folding of this peptide from extended to some virtually cyclic structure. It seemed reasonable to assume that this principle (or its generalized form) might be applicable to protein folding. A reaction path network was projected on the potential energy, and a continuous entropy surface was constructed under the condition of reduced dimensionality. The low entropy of the folded conformation indicated an information accumulation between 326% and 1414% with respect to the fully extended or unfolded structure. It is found that the location of existing and 'latent' critical points on the surface is revealed by the extrema and inflection points of the entropy curve.

Thermodynamic functions of conformational changes. 2. Conformational entropy as a measure of information accumulation.

Various folded molecular structures contain different amount of information. The relative amount of information may be related to relative entropy or entropy change. The conformational entropy change for n-butane has been computed as the function of rotation around the central C-C bond. It appears that the g+ or g- conformers contain about 16% more information than the anti-structure. Furthermore, the syn conformation with the two groups eclipsed contained about 42% more information than the fully staggered anti orientation. The conformational entropy function calculated from 3N - 7 internal degrees of freedom was found to be a continuous function.