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. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.

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. Mutations in the UBA domain, mainly in the highly conserved hydrophobic patch, induce conformational instabilities, which can be related to weak affinity for ubiquitin. This raises the question whether such hydrophobic patch presents conserved structural arrangement for selective recognition and protein binding. A concern that led us to investigate the stability of the p62-UBA domain as a case study regarding its structural arrangement as a function of temperature and two NaCl concentrations. Our results reveal that the temperature range and ionic strengths considered in this work produced a negligible effect on the three-helix bundle fold of p62-UBA domain.

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

We investigate the prevalence, and so the role in the amyloidogenesis, of biased conformations in large ensembles of monomeric forms for Aß42 and Aß40 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 Aß 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. The conformational ensembles generated by these intrinsically disordered peptides do not contain conformations highly similar to the amyloidogenic templates. This is a consequence of the low thermodynamic stability exhibited by the template-like conformations. A further constant-pH Monte Carlo study has revealed that this stability can be increased by suitable pH conditions, which helps to trigger the fibril elongation. Moreover, our analyses on the free energy landscapes, hydrogen bond prevalences, and principal component analysis distributions emphasize the relevance of many-body long-range cooperative interactions, likely acting over the infrequent preexisting structurally biased conformations, to explain the fibrils' emergence.

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+. To better elucidate how such properties might be systematically induced in rationally designed analogues, we performed comparative assessments of rIAPP, sIAPP, and sIAPP+ using replica-exchange molecular dynamics (REMD) with an accurate combination of force field Charmm22* and explicit aqueous solvation TIP4P/Ew. Our thermo-structural analyses show that sIAPP exhibits a thermal conversion channel of helices[Formula: see text]-sheets resembling hIAPP. This channel is depleted in rIAPP and is absent in sIAPP+. As a consequence, sIAPP+ presents an overall decrease of ß-like secondary structures and an overstabilization of α-helices. Additionally, we observed in rIAPP and sIAPP+ an increase in the backbone RMSF of molecular terminals and the exposed area of key residues. These structural features of sIAPP+ suggest a nonamyloidogenic character, which is corroborated by our judicious estimate of the electrostatic component of the solvation free energy using a generalized Born model, and so it may constitute an alternative strategy to sIAPP as a peptide analogue of hIAPP. Furthermore, our findings confirm that different aggregation propensities of amylin and its analogues are synergistically modulated by long-range effects of key mutations. Graphical Abstract S20R-Pramlintide.

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. The accurate force field Charmm22* with explicit aqueous solvation TIP4P/Ew ensured a minimal structural bias around physiological temperatures. Along which, the peptides are shown to present no structural-phase transition of folding from a microcanonical thermodynamics perspective. Both IAPP isoforms predominantly exhibit random-coil structures, but in a minor percentage we observed a direct α-helix → ß-sheet thermal conversion during the folding process of hIAPP, which is absent in pIAPP. The amyloidogenic segment 20-29 in pIAPP, which hosts 5 out of the 10 overall mutations found in this peptide, is strongly depleted of ß-sheet structures in constrast to hIAPP. Hydrogen bond analysis revealed a predominant frequency of 3-helix contacts in this residue range for pIAPP. These features of pIAPP anticorrelate with the presence of a well-known ß-sheet rich monomeric state that in hIAPP acts as an intermediate inducing oligomerization.

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

Structural properties of Aß(16-35) fragment are investigated as a model for the amyloid-ß 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 ß-sheet, without the long proposed helix intermediates. Our principal component analysis indicates that the fragment is also intrinsically disordered, as the full amyloid-ß peptide. Thus, the observed folding mechanism lacks free-energy barriers and any peaks in the thermal capacity.

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. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two Cα atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures.

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 ß-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid ß isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

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 = 0.85 and 1. Our analysis relies on the complex partition function zeros obtained with high statistics from multicanonical simulations. Finite size scaling relations for the leading partition function zeros yield critical exponents ν that are clearly consistent with a single second-order phase transition line, thus excluding such a tricritical point in that region of the phase diagram. This conclusion is further supported by analysis of the specific heat and susceptibility of the orientational order parameter.

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 ß(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. This topological feature corresponds to the communities in the graph.

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)=1.080(4) is found at the tricritical point.

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=2.215(2) and theta=-0.53(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., systems where a thermodynamic limit and exact results exist. Guided by this analysis we then discuss the helix-coil transition in polyalanine, an example of structural transitions in biological molecules.