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Nuclear translocation of large proteins is mediated through karyopherins, carrier proteins recognizing specific motifs of cargo proteins, known as nuclear localization signals (NLS). However, only few NLS signals have been reported until now. In the present work, NLS signals for Importins 4 and 5 were identified through an unsupervised in silico approach, followed by experimental in vitro validation. The sequences LPPRS(G/P)P and KP(K/Y)LV were identified and are proposed as recognition motifs for Importins 4 and 5 binding, respectively. They are involved in the trafficking of important proteins into the nucleus. These sequences were validated in the breast cancer cell line T47D, which expresses both Importins 4 and 5. Elucidating the complex relationships of the nuclear transporters and their cargo proteins is very important in better understanding the mechanism of nuclear transport of proteins and laying the foundation for the development of novel therapeutics, targeting specific importins.

The increased spectral range absorption of light exerted by pigments within Light Harvesting Complexes (LHCs) proves an important advantage under low light conditions, in higher plants. However, in the exposure to excess light, oxidative damages and ultimately cell death can occur. It proved, thus, utmost important for the photosynthetic organisms to develop a down-regulatory mechanism called NonPhotochemical Quenching (NPQ). Quantifying this mechanism at the atomic level is still very uncertain. There are several components of the photosynthetic apparatus that are actively involved in NPQ. Apart from the LHCs, and the xanthophyll cycle, the Photosystem II Subunit S (PsbS) is a 22-kDa integral membrane protein that is essential for the response of the photosynthetic apparatus to high-light and it is activated by the protonation of key lumen-exposed glutamate residues. Atomistic details on its involvement in NPQ remain still a mystery. However, It is widely accepted that NPQ (qE) is co-regulated by low lumen pH and ion fluxes (K+ , Ca2+, Mg2+ , Cl) in Lumen-Stroma areas. It has also been proposed that the activated PsbS may strongly interact with some LHCs enabling quenching by providing an alternative environment for some pigments within these LHCs, or by changing the membrane organization and dynamics. In this study, PsbS (pdb code 4ri2) is embedded in a lipid bilayer model membrane (400-500 POPC lipids, 1-palmitoyl-2-oleoyl-sn-glycero-3- phosphocholine). NPQ conditions are simulated by perturbations in the thylakoid lumen ionic load. Zeaxanthin (Zea) of the xanthophyll cycle that is produced under NPQ is also embedded in the membrane. We employ large-scale Molecular Dynamics simulations to probe the PsbS conformational changes, membrane dynamics, or Zea binding that activate PsbS. We identify two distinct PsbS forms (active-inactive), in response to A) the lumen acidification or ion fluxes, and B) the Zea binding, revealing a PsbSNPQ relation at the atomic scale.

The impact of aerosol properties on cloud dynamics and the radiative balance of the atmosphere relies on the parametrizations of cloud droplet formation. Such parametrization is based on equilibrium thermodynamics proposed by Köhler in 1936. There is considerable debate in the literature on the importance of factors like the surface tension depression or the water activity decrease for the correct parametrization. To gain fundamental insight into New Particle Formation (NPF), or Cloud Condensation Nuclei (CCN) activation one has to study microscopic properties of aqueous droplets, involving surface and bulk dynamics. The surface tension of droplets can be associated with the effects from Organic Matter (OM), whereas the static dielectric constant of water reflects the structure and dynamics of ions within solutions and can present a measure of water activity. In this study we employ Molecular Dynamics Simulations on aquatic droplets that contain surface active OM (acetaldehyde, methylglyoxal) and salts. We give insight into the dynamics of aquatic droplets with radials of 3.6nm at a level of detail that is not accessible experimentally (J. Phys. Chem. C 2016, 120:11508). We propose that as the surface tension of an aquatic droplet is decreased in the presence of surface-active OM, the water activity is affected as well. This is due to the fact that the water dipoles are oriented based on the salt morphology within the droplet. We suggest that the surface tension depression can be accompanied by the water activity change. This can be associated with the possible effects of surface-active species in terms of salt morphology transitions within an aerosol at the NPF and early particle growth time scales. Based on this study, surface-active OM seems important in controlling (a) the salt morphology transitions within a nucleus during NPF and particle growth and (b) a correlation between surface activity and water activity of ionic aquatic droplets. The latter correlation could be a fundamental property to consider when assessing NPF and the Köhler theory.

We have identified a ligand (CO) accommodation cavity in the signal transducer sensor protein HemAT (heme-based aerotactic transducer) that allows us to gain single-molecule insights into the mechanism of gas sensor proteins. Specific mutations that are distal and proximal to the heme were designed to perturb the electrostatic field near the ligand that is bound to the heme and near the accommodated ligand in the cavity. We report the detection of a second site in heme proteins in which the exogenous ligand is accommodated in an internal cavity. The conformational gate that directs the ligand-migration pathway from the distal to the proximal site of the heme, where the ligand is trapped, has been identified. The data provide evidence that the heme pocket is the specific ligand trap and suggest that the regulatory mechanism may be tackled starting from more than one position in the protein. Based on the results, we propose a dynamic coupling between the two distinct binding sites as the underlying allosteric mechanism for gas recognition/discrimination that triggers a conformational switch for signaling by the oxygen sensor protein HemAT. © 2006 by The National Academy of Sciences of the USA. 103 40 14796 14801 Cited By :26

Of the spectroscopic methods available for the characterization of the dynamics of heme protein active sites, time-resolved resonance Raman spectroscopy (TR3) is a powerful technique because excitation within the heme π-π* electronic absorption transitions selectively enhances vibrational modes of the heme and bound-proximal/distal ligands without the interference from the modes associated with the protein matrix. On the other hand, time-resolved step-scan (TRS2) Fourier transform infrared (FTIR) spectroscopy has the sensitivity and resolution to detect, in addition to ligands bound to metal centers and the kinetics of ligand photodissociation, transient changes at the level of individual amino acids during protein action. This review outlines the application of both TR 3 and TRS2-FTIR to heme-copper oxidases and nitric oxide reductases. Copyright © 2005 John Wiley & Sons, Ltd. 36 4 337 349 Cited By :5