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.

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.

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.

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.

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.

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 BS, quenching the crosslinking reaction, and binding the antibody-specific antigen.

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 HClO and HSiWO 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.

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.

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.

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.

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.

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.

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 β strands in a bilayered extended β-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids.

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.

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.

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.

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.

First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers.

First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti).

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.