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Biophysical Chemistry

Kehinde Onwochei Okonjo
Thirteen histidines and the α-chain terminal amino group (ACTA) make all of the contributions to the Bohr effect of human hemoglobin. The pKas of the 13 histidines in carbonmonoxy- and deoxyhemoglobin are known from (1)H NMR studies. Those of ACTA are not so precisely known. We employed the Wyman equation and the 13 histidine pairs of pKas to determine the pKas of ACTA by curve-fitting to hemoglobin Bohr effect data. Using all 14 pairs of pKas as preliminary data, we employed the Wyman equation to fit the Bohr data for hemoglobin chemically modified at Cys93β with cystamine, cystine and iodoacetamide...
April 18, 2017: Biophysical Chemistry
Shubhatam Sen, Monojit Chakraborty, Snigdha Goley, Swagata Dasgupta, Sunando DasGupta
The effect of oscillation induced by a frequency-dependent alternating current (AC) electric field to dissociate preformed amyloid fibrils has been investigated. An electrowetting-on-dielectric type setup has been used to apply the AC field of varying frequencies on preformed fibrils of human serum albumin (HSA). The disintegration potency has been monitored by a combination of spectroscopic and microscopic techniques. The experimental results suggest that the frequency of the applied AC field plays a crucial role in the disruption of preformed HSA fibrils...
April 13, 2017: Biophysical Chemistry
Liina Kangur, Michael R Jones, Arvi Freiberg
Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0...
April 7, 2017: Biophysical Chemistry
Carlos Henrique Dumard, Shana P C Barroso, Ana Clara V Santos, Nathalia S Alves, José Nelson S S Couceiro, Andre M O Gomes, Patricia S Santos, Jerson L Silva, Andréa C Oliveira
BACKGROUND: Avian influenza A viruses can cross naturally into mammals and cause severe diseases, as observed for H5N1. The high lethality of human infections causes major concerns about the real risk of a possible pandemic of severe diseases to which human susceptibility may be high and universal. High hydrostatic pressure (HHP) is a valuable tool for studies regarding the folding of proteins and the assembly of macromolecular structures such as viruses; furthermore, HHP has already been demonstrated to promote viral inactivation...
April 6, 2017: Biophysical Chemistry
Paola Cardiano, Francesco Crea, Claudia Foti, Ottavia Giuffrè, Silvio Sammartano
A potentiometric, UV and (1)H NMR study on Cu(2+)-ampicillin [(2S,5R,6R)-6-([(2R)-2-amino-2-phenylacetyl]amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid] and -amoxicillin [(2S,5R,6R)-6-{[(2R)-2-amino-2-(4-hydroxyphenyl)-acetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-24-carboxylic acid] systems in NaCl aqueous solution at I=0.15molL(-1) and t=25°C is reported. On the basis of potentiometric results two speciation models were proposed for each system. It was found that spectrophotometric and (1)H NMR measurements are essential for selecting the most reliable speciation models...
April 4, 2017: Biophysical Chemistry
Indu Sharma, Sudip K Pattanayek
The surface energy, a macroscopic property, depends on the chemical functionality and micro- and macroscopic roughness of the surface. The adsorption of two widely used proteins bovine serum albumin (BSA) and lysozyme on surfaces of four different chemical functionalities were done to find out the interrelation between macroscopic and microscopic properties. We have observed the secondary structure of protein after its adsorption. In addition, we observed the variation of surface energy of proteins due to variation in adsorption time, change in protein concentration and effect of a mixture of proteins...
April 1, 2017: Biophysical Chemistry
Masayoshi Nishiyama
High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa...
March 30, 2017: Biophysical Chemistry
Masaki Goto, Yuya Aoki, Nobutake Tamai, Hitoshi Matsuki
The phase transitions of N-methylated di-O-hexadecylphosphatidylethanolamines (DHPE, DH-N-methyl-PE (DHMePE) and DH-N,N-dimethyl-PE (DHMe2PE)) were observed by differential scanning calorimetry (DSC) and fluorometry under atmospheric pressure and by light-transmittance measurements under high pressure. The DSC thermograms showed that the N-methylated DHPE bilayers underwent the phase transition from the gel phase to the liquid crystalline (Lα) phase under atmospheric pressure. The gel phase was identified by fluorometry as the lamellar gel (Lβ) phase, and not interdigitated gel (LβI) phase...
March 30, 2017: Biophysical Chemistry
Matthias Karl, Michael Spoerner, Thuy-Vy Pham, Sunilkumar Puthenpurackal Narayanan, Werner Kremer, Hans Robert Kalbitzer
High pressure NMR spectroscopy is a powerful method for identifying rare conformational states of proteins from the pressure response of their chemical shifts. Many proteins have bound adenine nucleotides at their active centers, in most cases in a complex with Mg(2+)-ions. The (31)P NMR signals of phosphate groups of the nucleotides can be used as probes for conformational transitions in the proteins themselves. For distinguishing protein specific pressure effects from trivial pressure responses not due to the protein interaction, data of the pressure response of the free nucleotides must be available...
March 30, 2017: Biophysical Chemistry
Marzieh Saeedi, Alexander P Lyubartsev, Seifollah Jalili
To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center...
March 29, 2017: Biophysical Chemistry
Guilherme A P de Oliveira, Jerson L Silva
The combination of biophysical and structural techniques has allowed the visualization of species classified as dry molten-globule states. Further destabilization causes these structures to follow through a wet-globule stage to reach an unfolded chain. We have recently combined small angle X-ray scattering and nuclear magnetic resonance to observe these species, and we introduce a push-and-pull hypothesis to explain the dissimilar actions of urea and high pressure on proteins. The implications of these molten-globule states are further discussed in light of their potential physiological and pathological roles, especially in protein misfolding diseases...
March 29, 2017: Biophysical Chemistry
Elisa Gayán, Sander K Govers, Abram Aertsen
High hydrostatic pressure (HHP) is an important factor that limits microbial growth in deep-sea ecosystems to specifically adapted piezophiles. Furthermore, HHP treatment is used as a novel food preservation technique because of its ability to inactivate pathogenic and spoilage bacteria while minimizing the loss of food quality. Disruption of protein homeostasis (i.e. proteostasis) as a result of HHP-induced conformational changes in ribosomes and proteins has been considered as one of the limiting factors for both microbial growth and survival under HHP conditions...
March 21, 2017: Biophysical Chemistry
Petra Pullmannová, Ludmila Pavlíková, Andrej Kováčik, Michaela Sochorová, Barbora Školová, Petr Slepička, Jaroslav Maixner, Jarmila Zbytovská, Kateřina Vávrová
The Stratum corneum (SC) prevents water loss from the body and absorption of chemicals. SC intercellular spaces contain ceramides (Cer), free fatty acids (FFA), cholesterol (Chol) and cholesteryl sulfate (CholS). Cer with "very long" acyl chains (for example, N-lignoceroyl-sphingosine, CerNS24) are important for skin barrier function, whereas increased levels of "long" acyl Cer (for example, N-palmitoyl-sphingosine, CerNS16) occur in patients suffering from atopic eczema or psoriasis. We studied the impact of the replacement of CerNS24 by CerNS16 on the barrier properties and microstructure of model SC lipid membranes composed of Cer/FFA/Chol/CholS...
March 21, 2017: Biophysical Chemistry
Noa Erlitzki, Kenneth Huang, Suela Xhani, Abdelbasset A Farahat, Arvind Kumar, David W Boykin, Gregory M K Poon
Previous investigations of sequence-specific DNA binding by model minor groove-binding compounds showed that the ligand/DNA complex was destabilized in the presence of compatible co-solutes. Inhibition was interpreted in terms of osmotic stress theory as the uptake of significant numbers of excess water molecules from bulk solvent upon complex formation. Here, we interrogated the AT-specific DNA complex formed with the symmetric heterocyclic diamidine DB1976 as a model for minor groove DNA recognition using both ionic (NaCl) and non-ionic cosolutes (ethylene glycol, glycine betaine, maltose, nicotinamide, urea)...
March 20, 2017: Biophysical Chemistry
R N V Krishna Deepak, Brijesh Chandrakar, Ramasubbu Sankararamakrishnan
Metals play vital role in various physiological processes and are bound to biomolecules. Although cysteine sulfur is more frequently found as metal-binding ligand, methionine prefers to occur in copper-binding motifs of some proteins. To address methionine's lower preference in copper-binding sites in comparison to cysteine, we have considered copper-binding motifs (His-Cys-His-Met) from seven different high-resolution protein structures. We performed quantum chemical calculations to find out the strength of interactions between sulfur and metal ion in both Met and Cys residues...
March 18, 2017: Biophysical Chemistry
Liam Hovey, C Andrew Fowler, Ryan Mahling, Zesen Lin, Mark Stephen Miller, Dagan C Marx, Jesse B Yoder, Elaine H Kim, Kristin M Tefft, Brett C Waite, Michael D Feldkamp, Liping Yu, Madeline A Shea
Several members of the voltage-gated sodium channel family are regulated by calmodulin (CaM) and ionic calcium. The neuronal voltage-gated sodium channel NaV1.2 contains binding sites for both apo (calcium-depleted) and calcium-saturated CaM. We have determined equilibrium dissociation constants for rat NaV1.2 IQ motif [IQRAYRRYLLK] binding to apo CaM (~3nM) and (Ca(2+))4-CaM (~85nM), showing that apo CaM binding is favored by 30-fold. For both apo and (Ca(2+))4-CaM, NMR demonstrated that NaV1.2 IQ motif peptide (NaV1...
March 9, 2017: Biophysical Chemistry
Sunil Nath
Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis...
March 8, 2017: Biophysical Chemistry
Liyuan Niu, Kazuki Nomura, Hitoshi Iwahashi, Hiroyuki Matsuoka, Satoshi Kawachi, Yoshihisa Suzuki, Katsuhiro Tamura
Petit-High Pressure Carbon Dioxide (p-HPCD) is a promising nonthermal technology for foods pasteurization. Cluster analysis of gene expression profiles of Saccharomyces cerevisiae exposed to various stresses exhibited that gene expression profile for p-HPCD stress (0.5MPa, 25°C) was grouped into a cluster including profiles for Sodium Dodecyl Sulfate and Roundup herbicide. Both are detergents that can disorder membrane structurally and functionally, which suggests that cell membrane may be a target of p-HPCD stress to cause cell growth inhibition...
March 8, 2017: Biophysical Chemistry
Tomaz Urbic, Sara Najem, Cristiano L Dias
In this manuscript we use a two-dimensional coarse-grained model to study how amyloid fibrils grow towards an equilibrium state where they coexist with proteins dissolved in a solution. Free-energies to dissociate proteins from fibrils are estimated from the residual concentration of dissolved proteins. Consistent with experiments, the concentration of proteins in solution affects the growth rate of fibrils but not their equilibrium state. Also, studies of the temperature dependence of the equilibrium state can be used to estimate thermodynamic quantities, e...
March 7, 2017: Biophysical Chemistry
Gary J Robertson, Stoyan H Stoychev, Yasien Sayed, Ikechukwu Achilonu, Heini W Dirr
Glutathione S-transferase A3-3 is the most catalytically efficient steroid isomerase enzyme known in humans, transforming Δ(5)-androstene-3-17-dione into Δ(4)-androstene-3-17-dione. GSTA3-3 catalyzes this reaction with ten-fold greater efficiency than GSTA1-1, its closest competitor in the Alpha class of GSTs. In order to examine the differences between Alpha class GSTs and to better elucidate the mechanism of GSTA3-3 the roles of Tyr9 and Arg15 were examined. Tyr9 is the major catalytic residue of Alpha class GSTs and Arg15 is proposed to be catalytically important to GSTA3-3 but never before experimentally examined...
March 1, 2017: Biophysical Chemistry
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