Fluorapophyllite-(Cs), CsCa₄(Si₈O₂₀)F(H₂O)₈, a new apophyllite-group mineral from the Darai-Pioz Massif, Tien-Shan, Northern Tajikistan

Fluorapophyllite-(Cs) (IMA 2018-108a), ideally CsCa4(Si8O20)F(H2O)(8), is an apophyllite-group mineral from the moraine of the Darai-Pioz glacier, Tien-Shan, Northern Tajikistan. Associated minerals are quartz, pectolite, baratovite, aegirine, leucosphenite, pyrochlore, neptunite, fluorapophyllite-(K), and reedmergnerite. Fluorapophyllite-(Cs) is a hydrothermal mineral. It is colorless and has a vitreous luster and a white streak. Cleavage is perfect; it is brittle and has a stepped fracture. Mohs hardness is 4.5-5. D-meas. = 2.54(2) g/cm(3), D-calc. = 2.513 g/cm(3). Fluorapophyllite-(Cs) is unixial (+) with refractive indices (lambda = 589 nm) omega = 1.540(2), epsilon = 1.544(2). It is non-pleochroic. Chemical analysis by electron microprobe gave SiO2 48.78, Al2O3 0.05, CaO 22.69, Cs2O 10.71, K2O 1.13, Na2O 0.04, F 1.86, H2Ocalc. 14.61, -O=F2 -0.78, sum 99.09 wt.%; H2O was calculated from crystal-structure analysis. The empirical formula based on 29 (O + F) apfu, H2O = 8 pfu, is (Cs0.75K0.24)Sigma(0.99)(Ca3.99Na0.01)Sigma(4)(Si8.01Al0.01)Sigma 8.02O20.03F0.97(H2O)8, Z = 2. The simplified formula is (Cs,K)(Ca,Na)(4)(Si,Al) 8 O20F(H2O)(8). Fluorapophyllite-(Cs) is tetragonal, space group P4/mnc, a 9.060(6), c 15.741(11) angstrom, V 1292.10(19) angstrom(3). The crystal structure has been refined to R-1 = 4.31% based on 498 unique (F-o > 4 sigma F) reflections. In the crystal structure of fluorapophyllite-(Cs), there is one [4] T site occupied solely by Si,,T-O. = 1.615 angstrom. SiO4 tetrahedra link to form a (Si8O20)(8-)sheet perpendicular to [001]. Between the Si-O sheets, there are two cation sites: A and B. The A site is coordinated by eight H2O groups [O(4) site], A-O(4) = 3.152(4) angstrom; the A site contains Cs(0.75)K(0.24)A(0.01 square 0.01), ideally Cs apfu. The Cs-O bond length of 3.152 angstrom is definitely larger than the K-O bond length of 2.966-2.971 angstrom in fluorapophyllite-(K), KCa4(Si8O20)F(H2O)8. The [7]B site contains Ca3.99Na0.01, ideally Ca-4 apfu; < B-phi > = 2.417 angstrom (phi = O, F, H2O). The Si-O sheets connect via A and B polyhedra and hydrogen bonding; two H atoms have been included in the refinement. Fluorapophyllite-(Cs) is isostructural with fluorapophyllite-(K). Fluorapophyllite-(Cs) is a Cs-analogue of fluorapophyllite-(K)

Role of quantum coherence in chromophoric energy transport

The role of quantum coherence and the environment in the dynamics of excitation energy transfer is not fully understood. In this work, we introduce the concept of dynamical contributions of various physical processes to the energy transfer efficiency. We develop two complementary approaches, based on a Green's function method and energy transfer susceptibilities, and quantify the importance of the Hamiltonian evolution, phonon-induced decoherence, and spatial relaxation pathways. We investigate the Fenna-Matthews-Olson protein complex, where we find a contribution of coherent dynamics of about 10% and of relaxation of 80%.Comment: 5 pages, 3 figures, included static disorder, correlated environmen

Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation

The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.This research was funded by the Spanish Ministry of Science and Innovation and Ministry of Economy and Competitiveness and FEDER (EU): BIO2009-13261-C02-01/02 (ACA); BIO2012-39922-C02-01/02 (ACA); CTQ2013-4493 (JLN) and CSD2008-00005 (JLN); Andalusian Regional Government (Spain) and FEDER (EU): P09-CVI-5063 (ACA); and Valentian Regional Government (Spain) and FEDER (EU): Prometeo 2013/018 (JLN). Data collection was supported by European Synchrotron Radiation Facility (ESRF), Grenoble, France: BAG proposals MX-1406 (ACA) and MX-1541 (ACA); and ALBA (Barcelona, Spain) proposals 2012010072 (ACA) and 2012100378 (ACA)

Quantum entanglement in photosynthetic light harvesting complexes

Light harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long time scales despite the decohering effects of their environments. Within this context, we analyze entanglement in multi-chromophoric light harvesting complexes, and establish methods for quantification of entanglement by presenting necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson (FMO) protein to extract the initial state and temperature dependencies of entanglement. We show that while FMO in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amount of long-range and multipartite entanglement exists even at physiological temperatures. This constitutes the first rigorous quantification of entanglement in a biological system. Finally, we discuss the practical utilization of entanglement in densely packed molecular aggregates such as light harvesting complexes.Comment: 14 pages, 7 figures. Improved presentation, published versio

Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95

The relative promiscuity of hub proteins such as postsynaptic density protein-95 (PSD-95) can be achieved by alternative splicing, allosteric regulation, and post-translational modifications, the latter of which is the most efficient method of accelerating cellular responses to environmental changes in vivo. Here, a mutational approach was used to determine the impact of phosphorylation and succinimidation post-translational modifications on the binding affinity of the postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ3) domain of PSD-95. Molecular dynamics simulations revealed that the binding affinity of this domain is influenced by an interplay between salt-bridges linking the α3 helix, the β2–β3 loop and the positively charged Lys residues in its high-affinity hexapeptide ligand KKETAV. The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein. This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects. Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.This research was supported by grants CVI-05915, from the Andalusian Regional Government (http://www.juntadeandalucia.es), BIO2009-13261-C02 and BIO2012-39922-C02, from the Spanish Ministry of Science and Innovation (http://www.idi.mineco.gob.es/portal/site​/MICINN/) and FEDER. JMC received a postdoctoral contract from the Spanish Ministry of Science and Innovation. CCV was a recipient of a Formación de Personal Investigador fellowship from the Spanish Ministry of Science and Innovation