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Journal of Physical Chemistry. B

Sylwia Berbeć, Robert Dec, Dmitry Molodenskiy, Beata Wielgus-Kutrowska, Christian Johannessen, Agnieszka Hernik-Magoń, Fernando Tobias, Agnieszka Bzowska, Grzegorz Ścibisz, Timothy A Keiderling, Dmitri I Svergun, Wojciech Dzwolak
Replacing water with dimethyl sulfoxide (DMSO) completely reshapes the free-energy landscapes of solvated proteins. In DMSO, a powerful hydrogen-bond (HB) acceptor, formation of HBs between backbone NH groups and solvent is favored over HBs involving protein's carbonyl groups. This entails a profound structural disruption of globular proteins and proteinaceous aggregates (e.g. amyloid fibrils) upon transfer to DMSO. Here, we investigate an unusual DMSO-induced conformational transition of β2-amyloid fibrils from poly-L-glutamic acid (PLGA)...
November 14, 2018: Journal of Physical Chemistry. B
Peter A Eckert, Kevin J Kubarych
We report a spectroscopic investigation of the ultrafast dynamics of a second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(µ-S)(CO)3 ]2 . We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion which is absent from [Fe(µ-S)(CO)3 ]2 , and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers...
November 14, 2018: Journal of Physical Chemistry. B
Yifei Xu, Wendy Jessica Lin, Marisa Gliege, Ryan Gunckel, Zuofeng Zhao, Hongyu Yu, Lenore L Dai
Ionic liquids (ILs) show a promising future as electrolytes in electrochemical devices. In particular, IL based electrolytes bring operations at extreme temperatures to the realization that conventional electrolytes fail to accomplish. While IL electrolytes demonstrate considerable progresses in high-temperature applications, their breakthroughs in devices operating at low temperatures are still very limited due to undesirable phase transitions and unsatisfying transport properties. In this study, we present an approach that, by tuning molecular interactions in the system, the designed electrolyte of an IL based mixture can reach a lower operating temperature with improved transport properties...
November 13, 2018: Journal of Physical Chemistry. B
Xinchao Guan, Jiping Wang, Wenbing Hu
We performed dynamic Monte Carlo simulations to investigate the strain-induced polymer crystallization under separate enhancements of driving forces for homo-component and stereo-complex crystallization in the half-half symmetric racemic polymer blends. The results showed that polymer strain significantly enhances the stereo-complex crystallization, in comparison to the parallel cases of template-induced crystal growth without any strain in the previous simulations. We attributed the results to the strain-induced polymer crystallization favoring intermolecular crystal nucleation at high temperatures, which benefits the stereo-complex crystallization...
November 13, 2018: Journal of Physical Chemistry. B
Sujeet Dutta, Sowmya Srikantamurthy, Prabir Kumar Mukherjee, Subbarao Krishna Prasad
Bulk phase binary mixture of two rotator phase forming alkanes, n-Tricosane (C23H48) and n-Octacosane (C28H58) has been previously studied. C23H48 exists in the RII and RI phases, while C28H58 exists in the RIII and RIV phases. Over a certain range of composition, this binary mixture was found to exist in RII, RI and an intervening mesophase reported to be the hexatic phase, wherein the long-range two-dimensional in-plane hexagonal lattice order of the RII is lost and what remains is molecules present in hexagonal geometry without long-range positional correlation between individual hexagons...
November 13, 2018: Journal of Physical Chemistry. B
Małgorzata Jasiurkowska-Delaporte, Tomasz Rozwadowski, Ewelina Dmochowska, Ewa Juszyńska-Gałązka, Przemysław Kula, Maria Massalska-Arodź
This article presents the crystallization behavior and molecular dynamics of the supercooled nematic state of the newly synthesized liquid crystal 2,7-bis(4-pentylphenyl)-9,9-diethyl-9 H-fluorene (5P-EtFLEt-P5) studied by means of broadband dielectric spectroscopy (BDS). 5P-EtFLEt-P5 is a fragile glass-forming system with a high fragility parameter ( mf ≈ 121). The study compares the isothermal melt- and cold-crystallization processes at several selected temperatures Tc in the vicinity of the glass-transition temperature Tg (1...
November 13, 2018: Journal of Physical Chemistry. B
Leoncio Garrido, Inmaculada Aranaz, Alberto Gallardo, Carolina García, Nuria García, Esperanza Benito, Julio Guzman
November 12, 2018: Journal of Physical Chemistry. B
Xihong Xie, Yu-Shan Cheng, Meng-Hsuan Wen, Aparna Calindi, Karen Yang, Chi-Wei Chiu, Tai-Yen Chen
Transitions between different oligomeric states of membrane proteins are essential for proper cellular functions. However, the quantification of their oligomeric states in cells is technically challenging. Here we developed a new method to quantify oligomeric state(s) of highly expressed membrane proteins using the probability density function of molecule density ( PDFMD ) calculated from super-resolution localizations. We provided the theoretical model of PDFMD , discussed the effects of protein concentration, cell geometry, and photophysics of fluorescent proteins on PDFMD , and provided experimental criteria for proper quantification of oligomeric states...
November 12, 2018: Journal of Physical Chemistry. B
Mingdong Yao, Ying Liu, Liping Fei, Ye Zhou, Fangjun Wang, Jun Chen
The step of plastoquinone (PQ) reduction to plastoquinol (PQH2 ) can regulate the photoreaction rate of photosystem II (PSII). To experimentally unravel the PQ-PQH2 exchange mechanism of PSII, we investigate the reaction kinetics of plant PSII membranes and the subunits-trimmed PSII core complexes with various PQ analogues and directly probe the reductions of PQ and other quinones by 257 nm resonance Raman scattering. Two phases of quinone concentration effect on the reaction rate originate from the quinone-quinol exchange mechanism...
November 12, 2018: Journal of Physical Chemistry. B
Andrey S Mereshchenko, Olesya S Myasnikova, Pavel K Olshin, Sergey M Matveev, Maxim S Panov, Vladimir A Kochemirovsky, Mikhail Yu Skripkin, Alexander N Tarnovsky
Ultrafast excited-state dynamics of CuCl4 2- in acetonitrile is studied by femtosecond broadband transient absorption spectroscopy following excitation of the complex into all ligand-field (LF or d-d) states and into the two ligand-to-metal charge transfer (LMCT) states corresponding to the most intense steady-state absorption bands. The LF excited states are found to be nonreactive. The lowest-lying 2 E LF excited state has a lifetime less than 150 fs, and the lifetimes of the second (2 B1 ) and the third (2 A1 ) LF excited states are 1 and 5 ps, respectively...
November 12, 2018: Journal of Physical Chemistry. B
Yulian Gavrilov, Shlomi Dagan, Ziv Reich, Tali Scherf, Yaakov Levy
Previous studies conducted on flexible loop regions in proteins revealed that the energetic consequences of changing loop length predominantly arise from the entropic cost of ordering a loop during folding. However, in an earlier study of human acylphosphatase (hmAcP) using experimental and computational approaches, we showed that thermodynamic stabilization upon loop truncation can be attributed mainly to the increased entropy of the folded state. Here, using 15N NMR spectroscopy, we studied the effect of loop truncation on hmAcP backbone dynamics on the ps-ns timescale with the aim of confirming the effect of folded state entropy on protein stability...
November 9, 2018: Journal of Physical Chemistry. B
Steven A Yamada, Heather E Bailey, Michael D Fayer
Orientational pair correlations (OPCs), when they are sufficiently strong in a liquid, contain information on the interplay between structure and dynamics that arise from intermolecular interactions. Consequently, the quantification of OPCs remains a subject of substantial interest in current experimental and theoretical work. In the case of benzonitrile, the importance of OPCs remains ambiguous owing to the use of model-dependent analyses or reliance on a single spectroscopic technique. Here, IR polarization selective pump-probe (PSPP) and optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments were used to quantify OPCs in benzonitrile...
November 9, 2018: Journal of Physical Chemistry. B
Pannuru Kiran Kumar, Meena Bisht, Pannuru Venkatesu, Indra Bahadur, Eno E Ebenso
Enzymes are very important components which are vital for the existence of every cellular life. There is significant interest in the use of structurally stable and catalytically active enzymes in pharmaceutical, food, fine chemicals industries, and in various industrial processes as catalysts. Stem bromelain (BM) is a proteolytic enzyme which is widely used in chemical, medical, and pharmaceutical fields. However, harsh process conditions are the main barriers to the effective use of this enzyme in different applications...
November 9, 2018: Journal of Physical Chemistry. B
Nicole Fortoul, Maria Bykhovskaia, Anand Jagota
Neuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the presynaptic membrane. Vesicles are attached to the membrane via the SNARE complex, comprising the vesicle associated protein Synaptobrevin (Syb), the membrane associated protein syntaxin (Syx), and the cytosolic protein SNAP25 that together form a four-helical bundle. The full assembly of Syb onto the core SNARE bundle promotes vesicle fusion. We investigated SNARE assembly using a coarse-grained model of the SNARE complex that retains chemical specificity...
November 8, 2018: Journal of Physical Chemistry. B
Bob-Dan Lechner, Philip Biehl, Helgard Ebert, Stefan Werner, Annette Meister, Gerd Hause, Kirsten Bacia, Carsten Tschierske, Alfred Blume
Bolaamphiphiles are well known naturally occurring structures that can increase the thermal und mechanical stability of phospholipid membrane by incorporation in a trans-membrane manner. Modifications of bolaamphiphiles to introduce particular structural elements like a conjugated aromatic backbone and lateral side chains in the hydrophobic region lead to bolapolyphiles (BPs). We investigated the ability of BPs to form lyotropic phases in water. The BPs had identical backbone and side chains, but different headgroup structures leading to different abilities to act as hydrogen bond donors and acceptors...
November 8, 2018: Journal of Physical Chemistry. B
Fernando B da Silva, Vinícius G Contessoto, Vinícius M Martins de Oliveira, Jane Clarke, Vitor B P Leite
The energy landscape theory and the funnel description have a remarkable success in describing protein folding mechanisms and function. However, there are experimental results that are not understood using this approach. One of the puzzling examples are the α-spectrin results, in which the R15 domain folds three orders of magnitude faster than its homologous R16 and R17, even though they are structurally very similar to each other. Such anomalous observations are usually attributed to the influence of internal friction on protein folding rates, but this is not a satisfactory explanation...
November 8, 2018: Journal of Physical Chemistry. B
Feng Tao, Haiyan Liu
The Arabidopsis pyrabactin resistant 1 (PYR1)-like family of proteins (PYLs) are receptors of abscisic acid (ABA), an essential small signaling molecule in plants. Here we report a comparative molecular dynamics (MD) study on two PYL members, PYR1 and PYL10, which, despite their highly similar sequences and structures, have been suggested to belong to two different subclasses of PYLs, one being dimeric and relying on binding to ABA to inhibit downstream type 2C protein phosphatases (PP2Cs), the other being monomeric and able to constitutively inhibit downstream PP2Cs without ABA...
November 8, 2018: Journal of Physical Chemistry. B
Priya Rajdev, Suhrit Ghosh
This review article highlights utility of the Fluorescence Resonance Energy Transfer (FRET) to probe dynamics and related issues in amphiphilic polymeric aggregates and supramolecular polymers by spectroscopy and microscopy experiments. Amphiphilic polymers are attractive over small molecule amphiphiles because they exhibit significantly lower critical aggregation concentration, relatively larger particle size (suitable for Enhanced Permeation and Retention Effect) and much slower dynamics of exchange between the unimer and aggregate...
November 8, 2018: Journal of Physical Chemistry. B
Trent R Graham, David Semrouni, Eugene Mamontov, Anibal J Ramirez-Cuesta, Katharine Page, Aurora Evelyn Clark, Gregory K Schenter, Carolyn I Pearce, Andrew G Stack, Hsiu-Wen Wang
The (meta)stability of low water activity, sodium hydroxide/aluminate (Na+ OH- /Al(OH)4 - ) electrolytes dictates kinetics in the Bayer process for aluminum refining and high-level nuclear waste processing. We utilized quasi-elastic neutron scattering (QENS) and proton nuclear magnetic resonance spectroscopy (1 H NMR) to investigate the picosecond (ps) to microsecond (ms) timescale motions of H-bearing species (Al(OH)4 - monomers/clusters, OH- and H2 O) in extremely concentrated sodium aluminate solutions. In the QENS data, in contrast to typical liquids, no short-time translational diffusion was observed at 293 K, but two types of localized motions were found: (i) local backbone tumbling or a formation of large hydrated ion clusters on the order of 40-60 ps; and (ii) much slower, complex, collective dynamics of the ensemble of H-bearing species on the order of 350-750 ps...
November 8, 2018: Journal of Physical Chemistry. B
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