Conformations of proline analogues having double bonds in the ring

The intrinsic conformational preferences of proline analogues having double bonds between carbon atoms in their rings have been investigated using quantum mechanical calculations at the B3LYP/6-31+G(d,p) level. For this purpose, the potential energy surface of the N-acety-N'-methylamide derivatives of three dehydroprolines (proline analogues unsaturated at alpha,beta; beta,gamma; and gamma,delta) and pyrrole (proline analogue with unsaturations at both alpha,beta and gamma,delta) have been explored, and the results are compared with those obtained for the derivative of the nonmodified proline. We found that the double bonds affect the ring puckering and the geometric internal parameters, even though the backbone conformation was influenced the most. Results indicate that the formation of double bonds between carbon atoms in the pyrrolidine ring should be considered as an effective procedure to restrict the conformational flexibility of prolines. Interestingly, we also found that the N-acetyl-N'-methylamide derivative of pyrrole shows a high probability of having a cis peptide bond preceding the proline analogue.     

Coarse-graining the self-assembly of beta-helical protein building blocks

Nanotubular structures constructed using self-assembled beta-helical protein building blocks one atop the other have been coarsened to develop a mesoscopic potential that reproduces the intermolecular interaction energies provided by atomistic force-fields. The resulting potential consists of an analytical expression that depends exclusively on the distance and the relative orientation between the two interacting entities. In spite of its complexity, this coarse-grained potential reproduces satisfactorily the energetic properties of two interacting building blocks. The coarse-grained potential has been used to predict that the interaction between building blocks formed by residues 131-165 of E. coli galactoside acteyltransferase becomes repulsive when the size of the nanotube is larger than a threshold, that is, about 45 self-assembled building blocks.     

Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide

Recently a new non-coded amino acid was designed as a replacement for Arg, to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This constrained Arg analog, denoted c(5)Arg, was engineered to also promote the stability of the CREKA bioactive conformation. The conformational profile of the CREKA analog obtained by replacing Arg by c(5)Arg has been extensively investigated in this work. Two molecular dynamics simulations-based strategies have been employed: a modified simulated annealing and replica exchange. Results obtained using both techniques show that the conformational features of the new analog fulfill the purpose of its design. The new CREKA analog not only preserves the main structural attributes found for the bioactive conformation of the parent peptide but also shows lower flexibility. Moreover, the conformational profile of the mutated peptide narrows towards the most stable structures previously observed for the parent CREKA peptide.     

Effect of cation size and charge on the interaction between silica surfaces in 1:1, 2:1, and 3:1 aqueous electrolytes

Application of two complementary AFM measurements, force vs separation and adhesion force, reveals the combined effects of cation size and charge (valency) on the interaction between silica surfaces in three 1:1, three 2:1, and three 3:1 metal chloride aqueous solutions of different concentrations. The interaction between the silica surfaces in 1:1 and 2:1 salt solutions is fully accounted for by ion-independent van der Waals (vdW) attraction and electric double-layer repulsion modified by cation specific adsorption to the silica surfaces. The deduced ranking of mono- and divalent cation adsorption capacity (adsorbability) to silica, Mg(2+) < Ca(2+) < Na(+) < Sr(2+) < K(+) < Cs(+), follows cation bare size as well as cation solvation energy but does not correlate with hydrated ionic radius or with volume or surface ionic charge density. In the presence of 3:1 salts, the coarse phenomenology of the force between the silica surfaces as a function of salt concentration resembles that in 1:1 and 2:1 electrolytes. Nevertheless, two fundamental differences should be noticed. First, the attraction between the silica surfaces is too large to be attributed solely to vdW force, hence implying an additional attraction mechanism or gross modification of the conventional vdW attraction. Second, neutralization of the silica surfaces occurs at trivalent cation concentrations that are 3 orders of magnitude smaller than those characterizing surface neutralization by mono- and divalent cations. Consequently, when trivalent cations are added to our cation adsorbability series the correlation with bare ion size breaks down abruptly. The strong adsorbability of trivalent cations to silica contrasts straightforward expectations based on ranking of the cationic solvation energies, thus suggesting a different adsorption mechanism which is inoperative or weak for mono- and divalent cations.     

A strategy based on protein-protein interface motifs may help in identifying drug off-targets

Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network. In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface-based network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off-target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.     

Multichannel selective femtosecond coherent control based on symmetry properties

We present and implement a new scheme for extended multichannel selective femtosecond coherent control based on symmetry properties of the excitation channels. Here, an atomic nonresonant two-photon absorption channel is coherently incorporated in a resonance-mediated (2+1) three-photon absorption channel. By proper pulse shaping, utilizing the invariance of the two-photon absorption to specific phase transformations of the pulse, the three-photon absorption is tuned independently over an order-of-magnitude yield range for any possible two-photon absorption yield. Noticeable is a set of "two-photon dark pulses" inducing widely tunable three-photon absorption.     

Rectification of swimming bacteria and self-driven particle systems by arrays of asymmetric barriers

We show that the recent experimental observation of the rectification of swimming bacteria in a system with an array of asymmetric barriers occurs due to the ballistic component of the bacteria trajectories introduced by the bacterial "motor." Each bacterium selects a random direction for motion and then moves in this direction for a fixed period of time before randomly changing its orientation and moving in a new direction. In the limit where the bacteria undergo only Brownian motion on the size scale of the barriers, rectification does not occur. We examine the effects of steric interactions between the bacteria and observe a clogging effect upon increasing the bacteria density.     

Quark model relation for kaon charge radii

We derive the equation r²_E(K⁰)/r²_E(K⁺) = -(m²_s ? m²_n)/(2m²_s + m²_n) relating the kaon electric charge radii and the strange (m_s) and non-strange (m_n) quark masses in the nonrelativistic quark model, and suggest an inequality which we expect to hold in the presence of relativistic corrections. New data for these charge radii are presently being analysed by two experimental groups.     

Studies on the mass spectra of 6-methylthiopurine and its C-and N-methyl derivatives

6-Methylthiopurines which bear a 9-NH- or a 9-NCH₃-group (class A) form an [M—1]-ion with much higher abundance than do the 1-, 3-, or 7-methyl derivatives (class B). The higher stability of the [M—1]-ion in class A may be explained by ring closure to N-7. Methyl radicals are cleaved from N-, but not from S- or C-methyl groups, with the exception of the 7-methyl derivative, in which the S-CH₃-group can also split off a methyl radical. The methylthio group may lose all of the following fragments: S, SH, SCH, SCH₂ and SCH₃. In the remaining purine skeleton, in general first the pyrimidine and subsequently the imidazole ring breaks down with elimination of HCN.