Background:The mode of action of PI(4,5)P 2 in TRPV1 is controversial. Results: Positively charged amino acids in the S4-S5 linker and in the TRP box form the PI(4,5)P 2 binding site. Conclusion: PI(4,5)P 2 is a TRPV1 agonist and induces a conformational change of the internal gate. Significance: The molecular nature of the PI(4,5)P 2 binding site in TRPV1 is defined.

Alveolar stresses are fundamental to enable the respiration process in mammalians and have recently gained increasing attention due to their mechanobiological role in the pathogenesis and development of respiratory diseases. Despite the fundamental physiological role of stresses in the alveolar wall, the determination of alveolar stresses remains challenging, and our current knowledge is largely drawn from 2D studies that idealize the alveolar septal wall as a spring or a planar continuum. Here we study the 3D stress distribution in alveolar walls of normal lungs by combining ex-vivo micro-computed tomography and 3D finite-element analysis. Our results show that alveolar walls are subject to a fully 3D state of stresses rather than to a pure axial stress state. To understand the contributions of the different components and deformation modes, we decompose the stress tensor field into hydrostatic and deviatoric components, which are associated with isotropic and distortional stresses, respectively. Stress concentrations arise in localized regions of the alveolar microstructure, with magnitudes that can be up to 27 times the applied alveolar pressure. Interestingly, we show that the stress amplification factor strongly depends on the level of alveolar pressure, i.e, stresses do not scale proportional to the applied alveolar pressure. In addition, we show that 2D techniques to assess alveolar stresses consistently overestimate the stress magnitude in alveolar walls, particularly for lungs under high transpulmonary pressure. These findings take particular relevance in the study of stress-induced remodeling of the emphysematous lung and in ventilator-induced lung injury, where the relation between transpulmonary pressure and alveolar wall stress is key to understand mechanotransduction processes in pneumocytes.

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Glucansucrase GTF‐SI from Streptococcus mutans is a multidomain enzyme that catalyzes the synthesis of glucan polymers. Domain V locates 100 Å from the catalytic site and is required for an optimal activity. Nevertheless, the mechanism governing its functional role remains elusive. In this work, homology modeling and molecular dynamics simulations were employed to examine the effect of domain V in the structure and glucan‐binding ability of GTF‐SI in full and truncated enzyme models. Our results showed that domain V increases the flexibility of the α4′‐loop‐α4″ motif near the catalytic site resulting in a higher surface for glucan association, and modulates the orientation of a growing oligosaccharide (N=8‐23) in glucan‐enzyme complexes towards engaging in favorable contacts throughout the protein, whereas in the truncated model the glucan protrudes randomly from domain B towards the solvent. These results are valuable to increase understanding about the functional role of domain V in GH70 glucansucrases.

Laulimalide (LAU) and Peloruside A (PLA) are non-taxane microtubule stabilizing agents with promising antimitotic properties. These ligands promote the assembly of microtubules (MTs) by targeting a unique binding site on β-tubulin. The X-ray structure for LAU/PLA-tubulin association was recently elucidated, but little information is available regarding the role of these ligands as modulators of interdimeric interactions across MTs. Herein, we report the use of molecular dynamics (MD), principal component analysis (PCA), MM/GBSA-binding free energy calculations, and computational alanine scanning mutagenesis (ASM) to examine effect of LAU/PLA association on lateral and longitudinal contacts between tubulin dimers in reduced MT models. MD and PCA results revealed that LAU/PLA exerts a strong restriction of lateral and longitudinal interdimeric motions, thus enabling the stabilization of the MT lattice. Besides structural effects, LAU/PLA induces a substantial strengthening of longitudinal interdimeric interactions, whereas lateral contacts are less affected by these ligands, as revealed by MM/GBSA and ASM calculations. These results are valuable to increase understanding about the molecular features involved in MT stabilization by LAU/PLA, and to design novel compounds capable of emulating the mode of action of these ligands.

Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

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In this investigation, an optimal description of the structure–activity relationship was done for 59 σ1 receptor ligands including arylalkylaminoalcohols, arylalkenylamines, and arylalkylamines (denoted as RC‐33 analogs in this manuscript). We used optimal graph‐based (GBD) and Simplified Molecular Input Line Entry System (SMILES)‐based (SBD) descriptors as molecular characteristics of the structures to explain the differences in σ1 receptor affinity between the ligands. The best graph‐based descriptor model (named HFG‐EC0 in the manuscript) included hydrogen‐filled molecular graphs using the extended connectivity of zero order (EC0). This model has an average correlation coefficient value for external test set of 0.786 with a better statistics when comparing with the best SBD model. The best SBD model (named SSSk in the manuscript) includes only three SMILES elements SSSk and has an average correlation coefficient value for external test set of 0.726. These models identified the molecular features that contribute to a high σ1 receptor ligand affinity. Copyright © 2014 John Wiley & Sons, Ltd.