Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues.

Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors.

The high stability of the three-helix bundle UBA domain of p62 protein as revealed by molecular dynamics simulations.

The ubiquitin-associated (UBA) domain is an important motif in the modulation of many molecular functionalities. It has been mainly associated with ubiquitin-mediated proteolysis, a multistep mechanism in which undesirable proteins are tagged with polyubiquitin chains for degradation in the proteasome complex. Comparison among UBA domains reveals a quite small structural variability, displaying an overall fold with a tightly packed three-helix bundle, and a common conserved hydrophobic patch on their surface that is important for ubiquitin binding.

Occurrence of Biased Conformations as Precursors of Assembly States in Fibril Elongation of Amyloid-β Fibril Variants: An Study.

We investigate the prevalence, and so the role in the amyloidogenesis, of biased conformations in large ensembles of monomeric forms for Aβ42 and Aβ40 that can trigger the formation and growth of fibrils described by a dock-lock mechanism. We model such biased conformations as the structural monomeric units that constitute the Protein Data Bank fibrils 2beg, 2mxu, and 2lmn. These units were employed as templates to search for similar structures in statistical conformational ensembles of Aβ peptides generated by molecular dynamics with an accurate force field in explicit solvation, whose high quality is revealed by comparison with residual dipolar coupling (RDC) experiments.

Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues.

The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance might be improved by incorporating further mutations, as S20R, screened from the wild-type porcine isoform (pIAPP), which leads to the variant named sIAPP.

In Silico Comparative Study of Human and Porcine Amylin.

Islet transplantation is a promising treatment for type 2 diabetes, but its success is impaired by progressive graft loss, likely due to cytotoxic aggregation of the hormone human islet amyloid polypeptide (IAPP) secreted by the endocrine pancreas. Alternatively, the effectiveness of porcine xenotransplantations might be explained by the fibrillization-resistance of the porcine mutant. To better elucidate such molecular mechanisms, we performed comparative replica-exchange molecular dynamics simulations of both human (hIAPP) and porcine (pIAPP) isoforms.

Structural Interconversion in Alzheimer's Amyloid-β(16-35) Peptide in an Aqueous Solution.

Structural properties of Aβ(16-35) fragment are investigated as a model for the amyloid-β peptide excluding its coil-inducing terminals. Our replica-exchange molecular dynamics simulations using all-atom and explicit aqueous solvation widely reduce any structural bias. The principal folding pathway shows direct conversion of coil to β-sheet, without the long proposed helix intermediates.

Inferring a weighted elastic network from partial unfolding with coarse-grained simulations.

A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental Cα coordinates, and they only take the pairs of Cα atoms within a given cutoff distance rc into account.

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity.

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP).

Stripe-tetragonal phase transition in the two-dimensional Ising model with dipole interactions: partition function zeros approach.

We have performed multicanonical simulations to study the critical behavior of the two-dimensional Ising model with dipole interactions. This study concerns the thermodynamic phase transitions in the range of the interaction δ where the phase characterized by striped configurations of width h = 1 is observed. Controversial results obtained from local update algorithms have been reported for this region, including the claimed existence of a second-order phase transition line that becomes first order above a tricritical point located somewhere between δ = 0.

Communication: multicanonical entropy-like solution of statistical temperature weighted histogram analysis method.

A multicanonical update relation for calculation of the microcanonical entropy S(micro)(E) by means of the estimates of the inverse statistical temperature β(S), is proposed. This inverse temperature is obtained from the recently proposed statistical temperature weighted histogram analysis method (ST-WHAM). The performance of ST-WHAM concerning the computation of S(micro)(E) from canonical measures, in a model with strong free-energy barriers, is also discussed on the basis of comparison with the multicanonical simulation estimates.

Unveiling community structures in weighted networks.

Random walks on simple graphs in connection with electrical resistor networks lead to the definition of Markov chains with transition probability matrix in terms of electrical conductances. We extend this definition to an effective transition matrix Pij to account for the probability of going from vertex i to any vertex j of the original connected graph G. Also, we present an algorithm based on the definition of this effective transition matrix among vertices in the network to extract a topological feature related to the manner by which graph G has been organized.

Global persistence exponent of the two-dimensional Blume-Capel model.

The global persistence exponent theta(g) is calculated for the two-dimensional Blume-Capel model following a quench to the critical point from both disordered states and such with small initial magnetizations. Estimates are obtained for the nonequilibrium critical dynamics on the critical line and at the tricritical point. Ising-like universality is observed along the critical line and a different value theta(g)=1.

Universality and scaling study of the critical behavior of the two-dimensional Blume-Capel model in short-time dynamics.

In this paper we study the short-time behavior of the Blume-Capel model at the tricritical point as well as along the second order critical line. Dynamic and static exponents are estimated by exploring scaling relations for the magnetization and its moments at an early stage of the dynamic evolution. Our estimates for the dynamic exponents, at the tricritical point, are z=2.

Numerical comparison of two approaches for the study of phase transitions in small systems.

We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the cases of the q=4 and q=5 Potts model, i.e.