scholarly journals Isoelectric Point of Proteins at Hydrophobic Interfaces

2021 ◽  
Vol 9 ◽  
Author(s):  
Vanessa Lautenbach ◽  
Saman Hosseinpour ◽  
Wolfgang Peukert
Keyword(s):  
Isoelectric Point ◽  
Conformational Changes ◽  
Colloidal Stability ◽  
Hydrophobic Interactions ◽  
Ph Dependence ◽  
Hydration Shell ◽  
Hydrophobic Surface ◽  
Bulk Solution ◽  
Potential Measurement ◽  
Surfaces And Interfaces

Structural and colloidal stability of proteins at different surfaces and interfaces is of great importance in many fields including medical, pharmaceutical, or material science. Due to their flexibility, proteins tend to respond to their environmental conditions and can undergo structural and conformational changes. For instance, alterations in physiological factors such as temperature, ions concentration, or pH as well as the adsorption to an interface can initiate protein aggregation. Therefore, at different surfaces and interfaces the characterization of the structural and colloidal stability of proteins, which is mainly influenced by their electrostatic and hydrophobic interactions, is of fundamental importance. In this study, we utilized sum frequency generation (SFG) spectroscopy to assess the role of solution pH on the polarity and magnitude of the electric field within the hydration shell of selected model proteins adsorbed to a hydrophobic surface. We used polystyrene (PS) as a model hydrophobic surface and determined the isoelectric point (IEP) of four structurally different model proteins. Comparing the measured IEP of proteins at the PS/solution or air/solution interface with that determined in the bulk solution via zeta potential measurement, we found significant similarities between the IEP of surface adsorbed proteins and those in the bulk aqueous phase. The pH dependence behavior of proteins was correlated to their amino acid composition and degree of hydrophobicity.

Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽  
2021 ◽  
Author(s):  
Margrethe Gaardløs ◽  
Sergey A Samsonov ◽  
Marit Sletmoen ◽  
Maya Hjørnevik ◽  
Gerd Inger Sætrom ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Interdisciplinary Approach ◽  
Product Formation ◽  
Titration Calorimetry ◽  
Binding Groove ◽  
Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

scholarly journals pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

2010 ◽  
Vol 108 (1) ◽  
pp. 79-84 ◽  
Author(s):  
Magnus Johansson ◽  
Ka-Weng Ieong ◽  
Stefan Trobro ◽  
Peter Strazewski ◽  
Johan Åqvist ◽  
...  
Keyword(s):  
Ph Value ◽  
Ph Dependence ◽  
Peptide Bond ◽  
Bulk Solution ◽  
Peptide Bond Formation ◽  
Transfer Rates ◽  
Peptidyl Transfer ◽  
A Site ◽  
Rate Limiting ◽  
Site Binding

We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn, and Ile-tRNAIle, selected to cover a large range of intrinsic pKa-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, , at which the rate was half maximal. The -values were downshifted relative to the intrinsic pKa-value of aa-tRNAs in bulk solution. Gly-tRNAGly had the smallest downshift, while Ile-tRNAIle and Ala-tRNAAla had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pKa-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.

scholarly journals Carbon-Based Magnetic Nanocarrier for Controlled Drug Release: A Green Synthesis Approach

2018 ◽  
Vol 5 (1) ◽  
pp. 1 ◽  
Author(s):  
Jessica Oliveira ◽  
Raquel Rodrigues ◽  
Lillian Barros ◽  
Isabel Ferreira ◽  
Luís Marchesi ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Magnetic Nanoparticles ◽  
Drug Release ◽  
Phosphate Buffer ◽  
Colloidal Stability ◽  
Ph Dependence ◽  
Phosphate Buffer Solution ◽  
Controlled Drug Release ◽  
Buffer Solution ◽  
Carbon Based

In this study, hydrophilic magnetic nanoparticles were synthesized by green routes using a methanolic extract of Rubus ulmifolius Schott flowers. The prepared magnetic nanoparticles were coated with carbon-based shell for drug delivery application. The nanocomposites were further chemically functionalized with nitric acid and, sequentially, with Pluronic® F68 (CMNPs-plur) to enhance their colloidal stability. The resulting material was dispersed in phosphate buffer solution at pH 7.4 to study the Doxorubicin loading. After shaking for 48 h, 99.13% of the drug was loaded by the nanocomposites. Subsequently, the drug release was studied in different working phosphate buffer solutions (i.e., PB pH 4.5, pH 6.0 and pH 7.4) to determine the efficiency of the synthesized material for drug delivery as pH-dependent drug nanocarrier. The results have shown a drug release quantity 18% higher in mimicking tumor environment than in the physiological one. Therefore, this study demonstrates the ability of CMNPs-plur to release a drug with pH dependence, which could be used in the future for the treatment of cancer "in situ" by means of controlled drug release.

Sedimentation Properties of TiO2 Nanoparticles in Organic Solvents

2007 ◽  
Vol 119 ◽  
pp. 267-270 ◽  
Author(s):  
S.H. Woo ◽  
Min Ku Lee ◽  
Chang Kyu Rhee
Keyword(s):  
Tio2 Nanoparticles ◽  
Organic Solvents ◽  
Colloidal Stability ◽  
Light Flux ◽  
Particle Growth ◽  
Potential Measurement ◽  
Tio2 Particles ◽  
Sedimentation Behavior ◽  
Flux Profile ◽  
Particle Coalescence

In this study, the colloidal stability and sedimentation behavior of crystalline TiO2 particles (∼300nm) in various organic solvents have been investigated by means of a backscattered light flux profile (Turbiscan) and a zeta potential measurement. The backscattered light flux profiles revealed that the TiO2 nanoparticles were readily sedimented in water, methyl alcohol, and ethyl alcohol due to a flocculation-induced particle growth, while a particle coalescence and a sedimentation of the TiO2 nanoparticles were hardly observed in isopropyl alcohol. The measured ζ potentials verified the differences of the colloidal stabilities of the TiO2 particles in the organic solvents, showing a good correlation with the migration velocity.

scholarly journals Antidepressants are modifiers of lipid bilayer properties

2019 ◽  
Vol 151 (3) ◽  
pp. 342-356 ◽  
Author(s):  
Ruchi Kapoor ◽  
Thasin A. Peyear ◽  
Roger E. Koeppe ◽  
Olaf S. Andersen
Keyword(s):  
Membrane Protein ◽  
Lipid Bilayer ◽  
Conformational Changes ◽  
Partition Coefficients ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Conformational Transition ◽  
Hydrophobic Interactions ◽  
Energetic Cost ◽  
Titration Calorimetry ◽  
Channel Activity

The two major classes of antidepressants, tricyclic antidepressants (TCAs) and selective serotonin reuptake inhibitors (SSRIs), inhibit neurotransmitter reuptake at synapses. They also have off-target effects on proteins other than neurotransmitter transporters, which may contribute to both desired changes in brain function and the development of side effects. Many proteins modulated by antidepressants are bilayer spanning and coupled to the bilayer through hydrophobic interactions such that the conformational changes underlying their function will perturb the surrounding lipid bilayer, with an energetic cost (ΔGdef) that varies with changes in bilayer properties. Here, we test whether changes in ΔGdef caused by amphiphilic antidepressants partitioning into the bilayer are sufficient to alter membrane protein function. Using gramicidin A (gA) channels to probe whether TCAs and SSRIs alter the bilayer contribution to the free energy difference for the gramicidin monomer⇔dimer equilibrium (representing a well-defined conformational transition), we find that antidepressants alter gA channel activity with varying potency and no stereospecificity but with different effects on bilayer elasticity and intrinsic curvature. Measuring the antidepressant partition coefficients using isothermal titration calorimetry (ITC) or cLogP shows that the bilayer-modifying potency is predicted quite well by the ITC-determined partition coefficients, and channel activity is doubled at an antidepressant/lipid mole ratio of 0.02–0.07. These results suggest a mechanism by which antidepressants could alter the function of diverse membrane proteins by partitioning into cell membranes and thereby altering the bilayer contribution to the energetics of membrane protein conformational changes.

scholarly journals Towards Building Blocks for Supramolecular Architectures Based on Azacryptates

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1733 ◽  
Author(s):  
Ana Miljkovic ◽  
Sonia La Cognata ◽  
Greta Bergamaschi ◽  
Mauro Freccero ◽  
Antonio Poggi ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Building Blocks ◽  
Water Mixture ◽  
Molecular Systems ◽  
Supramolecular Architectures ◽  
Starting Point ◽  
The Difference ◽  
Supramolecular Devices

In this work, we report the synthesis of a new bis(tris(2-aminoethyl)amine) azacryptand L with triphenyl spacers. The binding properties of its dicopper complex for aromatic dicarboxylate anions (as TBA salts) were investigated, with the aim to obtain potential building blocks for supramolecular structures like rotaxanes and pseudo-rotaxanes. As expected, UV-Vis and emission studies of [Cu2L]4+ in water/acetonitrile mixture (pH = 7) showed a high affinity for biphenyl-4,4′-dicarboxylate (dfc2−), with a binding constant of 5.46 log units, due to the best match of the anion bite with the Cu(II)-Cu(II) distance in the cage’s cavity. Compared to other similar bistren cages, the difference of the affinity of [Cu2L]4+ for the tested anions was not so pronounced: conformational changes of L seem to promote a good interaction with both long (e.g., dfc2−) and short anions (e.g., terephthalate). The good affinity of [Cu2L]4+ for these dicarboxylates, together with hydrophobic interactions within the cage’s cavity, may promote the self-assembly of a stable 1:1 complex in water mixture. These results represent a good starting point for the application of these molecular systems as building units for the design of new supramolecular architectures based on non-covalent interactions, which could be of interest in all fields related to supramolecular devices.

scholarly journals De novo design of tunable, pH-driven conformational changes

Science ◽  
2019 ◽  
Vol 364 (6441) ◽  
pp. 658-664 ◽  
Author(s):  
Scott E. Boyken ◽  
Mark A. Benhaim ◽  
Florian Busch ◽  
Mengxuan Jia ◽  
Matthew J. Bick ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Mammalian Cells ◽  
Large Scale ◽  
Environmental Changes ◽  
De Novo ◽  
Hydrophobic Interactions ◽  
De Novo Design ◽  
General Strategy ◽  
Histidine Residues ◽  
Hydrogen Bond Networks

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

A pH-dependent conformational transition of Aβ peptide and physicochemical properties of the conformers in the glial cell

2002 ◽  
Vol 361 (3) ◽  
pp. 547-556 ◽  
Author(s):  
Yoichi MATSUNAGA ◽  
Nobuhiro SAITO ◽  
Akihiro FUJII ◽  
Junichi YOKOTANI ◽  
Tadakazu TAKAKURA ◽  
...  
Keyword(s):  
Glial Cell ◽  
Conformational Changes ◽  
Conformational Transition ◽  
Early Stage ◽  
Ph Dependence ◽  
Amyloid Β ◽  
Proteinase K ◽  
Aβ Peptide ◽  
Ph Dependent ◽  
Insight Into

In the present study we identified the epitopes of antibodies against amyloid β-(1–42)-peptide (Aβ1–42): 4G8 reacted with peptides corresponding to residues 17–21, 6F/3D reacted with peptides corresponding to residues 9–14, and anti 5-10 reacted with peptides corresponding to residues 5–10. The study also yielded some insight into the Aβ1–42 structures resulting from differences in pH. An ELISA study using monoclonal antibodies showed that pH-dependent conformational changes occur in the 6F/3D and 4G8 epitopes modified at pH 4.6, but not in the sequences recognized by anti 1-7 and anti 5-10. This was unique to Aβ1–40 and Aβ1–42 and did not occur with Aβ1–16 or Aβ17–42. The reactivity profile of 4G8 was not affected by blockage of histidine residues of pH-modified Aβ1–40 and Aβ1–42 with diethyl pyrocarbonate; however, the mutant [Gln11]Aβ1–40 abrogated the unique pH-dependence towards 4G8 observed with Aβ1–40. These findings suggest that these epitopes are cryptic at pH4.6, and that Glu11 is responsible for the changes. We suggest that the abnormal folding of 6F/3D epitope affected by pH masked the 4G8 epitope. A study of the binding of metal ions to Aβ1–42 suggested that Cu2+ and Zn2+ induced a conformational transition around the 6F/3D region at pH7.4, but did not affect the region when it was modified at pH4.6. However, Fe2+ had no effect, irrespective of pH. Aβ modified at pH 4.6 appeared to be relatively resistant to proteinase K compared with Aβs modified at pH7.4, and the former might be preferentially internalized and accumulated in a human glial cell. Our findings suggest the importance of microenvironmental changes, such as pH, in the early stage of formation of Aβ aggregates in the glial cell.

Sign in / Sign up

Export Citation Format

Share Document