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Journal of Physical Chemistry. B

Nicole L Ing, Mohamed Y El-Naggar, Allon I Hochbaum
Bioelectronic materials interface biomolecules, cells, organs, or organisms with electronic devices, and they represent an active and growing field of materials research. Protein and peptide nanostructures are ideal bioelectronic materials. They possess many of the properties required for biocompatibility across scales from enzymatic to organismal interfaces, and recent examples of supramolecular protein and peptide nanostructures exhibit impressive electronic properties. The ability of such natural and synthetic protein and peptide materials to conduct electricity over μm to cm length scales, however, is not readily understood from a conventional view of their amino acid building blocks...
September 21, 2018: Journal of Physical Chemistry. B
Benjamin Paul Wiebenga-Sanford, Jack B Washington, Brett Cosgrove, Eduardo F Palomares, Derrick A Vasquez, Christopher D Rithner, Nancy E Levinger
The research presented here reports the surprising observation that adding glucose and other carbohydrate osmolytes to the polar phase of water-containing reverse micelles causes the particles to shrink. This apparent change in reverse micelle size is attributed to two factors: an increase in surface area per surfactant molecule induced by the presence of carbohydrate and changes in the particle shape eccentricity. The studies reported here focus on glucose but also explore other carbohydrate osmolytes, specifically ethylene glycol, glycerol, erythritol, xylitol, sorbitol, myo-inositol, and trehalose, in the nanoconfined environments of reverse micelles...
September 21, 2018: Journal of Physical Chemistry. B
Pablo Orcid- Turjanski, Diego Ulises Ferreiro
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for 'repetition', an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures...
September 21, 2018: Journal of Physical Chemistry. B
Mateusz Zbigniew Brela, Piotr Kubisiak, Andrzej Eilmes
Analysis of the hydrogen bond network in aprotic ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide has been performed based on structures obtained from ab initio or classical molecular dynamics simulations. Statistics of different donor and acceptor atoms and the amount of chelating or bifurcated bonds has been presented. Most of hydrogen bonds in EMIM-TFSI are formed with oxygen atom as hydrogen acceptors; and the most probable bifurcated bonds are those with a mixed pair of oxygen and nitrogen acceptors...
September 21, 2018: Journal of Physical Chemistry. B
Paween Mahinthichaichan, Dylan M Morris, Yi Wang, Grant J Jensen, Emad Tajkhorshid
Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semipermeable central pores containing binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO3 - (the dominant form of CO2 in the aqueous solution at pH 7.4) but not O2 , which leads to a nonproductive reaction. To test this hypothesis, here we use molecular dynamics simulations to characterize the energetics and permeability of CO2 , O2 , and HCO3 - through the central pores of two different shell proteins, namely, CsoS1A of α-carboxysome and CcmK4 of β-carboxysome shells...
September 21, 2018: Journal of Physical Chemistry. B
Abhishek K Sharma, Fernando A Escobedo
Monte Carlo simulations are used to investigate the mechanism of the disorder-to-order phase transition for a bulk system of colloidal hard cubes. It is observed that the structure of the ordered state is foreshadowed in the disordered state through multiple spontaneously occurring ordered domains. Such domains arise due to the entropic preference for local facet alignment between particles and occur transiently and sparsely throughout the system even in the stable isotropic phase. At pressures (and degrees of supersaturation) where the isotropic phase becomes marginally metastable, a classical nucleation process is never observed; instead, the ordered domains increase in number and size, eventually reaching a critical point where they percolate the entire system and spontaneously consolidate to form the ordered phase...
September 21, 2018: Journal of Physical Chemistry. B
Akira Naito, Shunsuke Kametani, Akihiro Aoki, Tetsuo Asakura
Poly-L-alanine (PLA) sequences are key elements of the crystalline domains of spider dragline and wild silkworm silks. In the present work,1 H spin diffusion 2D correlation NMR spectra were observed for selectively deuterated (Ala)3 and (Ala)4 crystals to develop the analytical method for the structure of PLA sequences. The build-up curves of the cross peaks for three kinds of 1 H pairs in selectively deuterated (Ala)3 and (Ala)4 crystals were observed to obtain spin diffusion rate constant kj,k from relaxation master equations Pi,j (τm )...
September 20, 2018: Journal of Physical Chemistry. B
Vishram L Terse, Shachi Gosavi
Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a Cα-level (Cα-SBM) and found that the simulated folding route did not agree with the experimentally observed one. Simulating the Cα-SBM with a cut-off contact map, instead of a screened contact map, switched the folding route with the new route matching the experimental route. Thus, the simulated folding of ubiquitin is sensitive to contact map definition...
September 20, 2018: Journal of Physical Chemistry. B
Yonatan Biniuri, Bauke Albada, Itamar Willner
Microscale thermophoresis (MST) is used to follow the dissociation constants corresponding to ATTO 488-labeled adenosine triphosphate (ATP) and the ATP-aptamer or ATP-aptamer mutants that include two binding sites for the ATP ligand. A set of eight ATP-aptamer mutants, where the thymidine bases, within the reported ATP binding aptamer sites, are substituted with cytosine bases, are examined. The MST-derived dissociation constant of ATP to the reported aptamer is Kd = 31 ± 3 μM, whereas most of the aptamer mutants show lower affinity (higher Kd values) toward the ATP ligand...
September 20, 2018: Journal of Physical Chemistry. B
Zhixin Guo, Shuya Li, Xueying Liu, Jie Zhang, Huihui Li, Xiaoli Sun, Zhongjie Ren, Shouke Yan
Through fixing the orientation of oriented PE thin film during melt-recrystallization with the help of a vacuum evaporated thin carbon layer, the isothermal melt- and cold-crystallization of iPMMA on oriented PE substrate was studied. The results show that same parallel chain epitaxy of iPMMA on oriented PE substrate takes place in both cold- and melt-crystallization processes based on a two-dimensional lattice matching. However, the crystallization kinetics in the two processes is quite different. The induction time of iPMMA during melt-crystallization is significantly longer than during cold-crystallization (11 h vs 2...
September 19, 2018: Journal of Physical Chemistry. B
Fernando M Boubeta, Leonardo Boechi, Dario A Estrin, Barbara Patrizi, Mariangela Di Donato, Alessandro Iagatti, Daniela Giordano, Cinzia Verde, Stefano Bruno, Stefania Abbruzzetti, Cristiano Viappiani
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites has been associated to cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins - a family of microbial heme-proteins of yet-unclear function - applying Molecular-Dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue...
September 19, 2018: Journal of Physical Chemistry. B
Abdelkrim Benabbas, Paul M Champion
The dynamics of methionine geminate recombination following photo-dissociation in ferrous cytochrome c is investigated over a broad temperature range. The kinetic response, above the solvent glass transition (Tg ), is nearly mono-exponential and displays a weak temperature dependence. Below Tg , the rebinding kinetics are non-exponential and can be explained using a quenched distribution of enthalpic rebinding barriers, arising from a relatively narrow distribution of heme out-of-plane displacements. The Arrhenius prefactor of this ΔS=2 reaction is ~1011 s-1, which is similar to what has been found for the ΔS=1 NO binding reaction in heme proteins...
September 19, 2018: Journal of Physical Chemistry. B
Valery Nguemaha, Sanbo Qin, Huan-Xiang Zhou
The malleability of intrinsically disordered proteins (IDPs) has generated great interest in understanding how their conformations respond to crowded cellular environments. Experiments can report gross properties such as fluorescence resonance energy transfer (FRET) efficiency, but cannot resolve the conformational ensembles of IDPs and their interactions with macromolecular crowders. Computation can in principle provide the latter information but in practice has been hampered by the enormous expense for realistic modeling of IDPs and crowders and for sufficient conformational sampling...
September 19, 2018: Journal of Physical Chemistry. B
Peter J Steinbach
A continuum solvent model based on screened Coulomb potentials has been simplified and parameterized to sample native-like structures in replica-exchange simulations of each of six different peptides and mini-proteins. Low-energy, native and non-native structures were used to iteratively refine eleven parameter values. The centroid of the largest cluster of structures sampled in simulations initiated from an extended conformation represents the predicted structure. The main-chain rms deviation of this prediction from the experimental structure was 0...
September 19, 2018: Journal of Physical Chemistry. B
Janghyun Yoo, John M Louis, Irina V Gopich, Hoi Sung Chung
We describe the theory, and experimental and analysis methods of three-color Förster resonance energy transfer (FRET) spectroscopy for probing conformational dynamics of a fast-folding protein, α3 D. In three-color FRET, site-specific labeling of fluorophores is required to avoid ambiguity resulting from various species with different combinations of labeling positions. To this end, we attached two dyes to a cysteine residue and an unnatural amino acid first, and then appended a cysteine residue to the C-terminus of the protein by the sortase-mediated ligation for attaching the third dye...
September 19, 2018: Journal of Physical Chemistry. B
Hujun Shen, Zhenhua Wu, Mingsen Deng, Shuiguo Wen, Chenggui Gao, Shixiong Li, Xupu Wu
Membrane Dipole potential influences a variety of important biological processes involving cell membranes. Since it is quite challenging to directly measure the membrane dipole potential in experiments, molecular dynamics (MD) simulation has emerged as a powerful tool for a reasonable prediction of the dipole potential. Although MD predictions agree well with experiment about the sign of dipole potential, the magnitude of dipole potential varies significantly with the force field parameters. It has been shown that the positive dipole potential of PC bilayer membranes would be overestimated by a non-polarizable model owing to the treatment of many-body polarization effects in a mean-field fashion...
September 19, 2018: Journal of Physical Chemistry. B
Lukasz Skorka, Vincent Maurel, Jacek B Gosk, Roman Puzniak, Jean-Marie Mouesca, Irena Kulszewicz-Bajer
Arylamine moieties oxidized to radical cations are considered promising spin bearing units in high-spin type compounds. Here, we report the first use of carbazole-3,6-diamine units as efficient rigid spin containing units. The use of rigid spin bearing units enhances significantly spin exchange interactions. The design using DFT calculations shows the progressive increase of the exchange coupling constant dependent on the considered model molecules. Two of the most representative molecules containing flexible (dimer 1) and rigid spin coupling unit (dimer 2) were synthesized...
September 19, 2018: Journal of Physical Chemistry. B
Heather E Bailey, Yong-Lei Wang, Stephen R Lynch, Michael D Fayer
The orientational dynamics and microscopic structures of nicotine/water binary mixtures near the system's lower critical solution temperature (LCST) were elucidated using optical heterodyne-detected optical Kerr effect (OHD-OKE) spectroscopy, nuclear magnetic resonance correlation spectroscopy (COSY), first-principles calculations and MD simulations. Water concentrations were investigated from zero to close to pure water. At temperatures below the LCST, OHD-OKE experiments measured an anomalous slowing as the phase transition concentration was approached...
September 19, 2018: Journal of Physical Chemistry. B
Geraldine S Lim, Marco Klähn
The stability of two small proteins, one composed of three α-helices (α-peptide) and another composed of a β-sheet (β-peptide) solvated in five different ionic liquids (ILs), is analyzed using replica exchange molecular dynamics (REMD) simulations. ILs are composed of 1-butyl-3-methylimidazolium (BMIM) cations, paired with five different anions of varying hydrophilicity and size, namely, Cl- , NO3 - , BF4 - , PF6 - , and NTf2 - . REMD simulations greatly improve structure sampling and mitigate bias toward the initial folded peptide structure, thereby providing more adequate simulations to study protein stability...
September 19, 2018: Journal of Physical Chemistry. B
Renee Vancraenenbroeck, Hagen Hofmann
Quantifying the stability of intermediates along parallel molecular pathways is often hampered by the limited experimental resolution of ensemble methods. In biology, however, such intermediates may represent important regulatory targets, thus calling for strategies to map their abundance directly. Here, we use single-molecule Förster resonance energy transfer (FRET) to quantify the occupancies of intermediates along two parallel DNA-binding pathways of the basic helix-loop-helix leucine-zipper (bHLH-LZ) domains of the transcription factors c-Myc and Max...
September 19, 2018: Journal of Physical Chemistry. B
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