scholarly journals NMR Structures of ApoL. caseiDihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions

Biochemistry ◽  
2011 ◽  
Vol 50 (18) ◽  
pp. 3609-3620 ◽  
Author(s):  
James Feeney ◽  
Berry Birdsall ◽  
Nadezhda V. Kovalevskaya ◽  
Yegor. D. Smurnyy ◽  
Emna M. Navarro Peran ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Cooperative Binding ◽  
Nmr Structures

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 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.

scholarly journals Lectins-glycoconjugates interactions: Experimental and computational docking studies of the binding and agglutination of eight different lectins in a comparative manner

2020 ◽  
Author(s):  
Amit Kumar ◽  
Vijaya Kumar Hinge ◽  
Ashapogu Venugopal ◽  
Siva Kumar Nadimpalli ◽  
Chebrolu Pulla Rao
Keyword(s):  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Cd Spectroscopy ◽  
Docking Studies ◽  
Model Systems ◽  
Computational Docking ◽  
Differential Recognition ◽  
Polar Interactions ◽  
Lectin Specificity ◽  
Comparative Manner

ABSTRACTAltering the lectin properties by chemically synthesized glycoconjugates is important in glycobiology. A series of eight plant lectins with varying carbohydrate specificity were chosen as model systems to study the binding by synthetic glycoconjugates. One of our earlier paper 1 deals with the binding of glycoconjugates by jacalin. Further to this, we have now extended the studies to several other lectins having specificities towards glucose/mannose, galactose and lactose, and the results are reported in this paper on a comparative manner. The binding aspects were established by hemagglutination and fluorescence spectroscopy, and the conformational changes by CD spectroscopy. Out of the fourteen glycoconjugates used in the present study, a galactosyl-naphthyl derivative, 1c turns out to be most effective towards galactose-specific lectin in agglutination inhibition, fluorescence quenching by inducing considerable conformational changes. Similarly, mannosyl-naphthyl derivative, 3c turns out to be most effective in inhibiting the agglutination of Glc/Man specific lectins. Present study demonstrates differential recognition of conjugates towards lectins. The results also supported the existence of a correlation between the glycoconjugate and lectin specificity at the carbohydrate recognition domain (CRD). The glycoconjugate that inhibits the agglutination binds in the CRD via polar interactions as well as by nonpolar/hydrophobic interactions arising from the aromatic moiety of the conjugate, whereas, the non-inhibiting conjugates bind primarily via hydrophobic interactions. The specific and selective binding of the glycoconjugates by these lectins were proven by the docking studies. Thus, the present study has contributed immensely towards understanding the molecular interactions present between the lectins and small molecules that will eventually help better drug design where the presence of hydrophoibic moieties would play important role.

scholarly journals Investigation on the Binding and Conformational Change of All-trans-Retinoic Acid with Peptidyl Prolyl cis/trans Isomerase Pin1 Using Spectroscopic and Computational Techniques

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
GuoFei Zhu ◽  
ShaoLi Lyu ◽  
Yang Liu ◽  
Chao Ma ◽  
Wang Wang
Keyword(s):  
Retinoic Acid ◽  
Conformational Change ◽  
Conformational Changes ◽  
Fluorescence Spectra ◽  
Hydrophobic Interactions ◽  
Binding Constants ◽  
Principal Component ◽  
Computational Techniques ◽  
Trans Retinoic Acid ◽  
All Trans Retinoic Acid

Binding and conformational change of all-trans-retinoic acid (ATRA) with peptidyl prolyl cis/trans isomerase Pin1 were investigated systematically by spectroscopic and computational techniques under experimentally optimized physiological conditions. The intrinsic fluorescence of Pin1 was quenched through a static quenching mechanism in the presence of ATRA with binding constants on the order of 105 mol/L. Thermodynamic parameters (ΔH = 15.76 kJ/mol and ΔS = 158.36 J/mol·K at 293 K) and computational results illustrated that the hydrophobic interactions played a significant role in the binding process of ATRA to Pin1, but electrostatic forces, weak van der Waals, and hydrogen bonds cannot be ignored. Circular dichroism, fluorescence spectra, and computational simulations revealed that ATRA interacted with residues Lys63 and Arg69 of Pin1 to affect its conformational changes. Molecular dynamic simulation, principal component analysis, and free energy landscape monitored the dynamical conformational characteristics of ATRA binding to Pin1. All in all, the present research might provide a reference for the development and design of retinoic acid drugs that inhibit the activity of Pin1.

scholarly journals Computational modeling reveals a hydrophobic force-induced pore-forming mechanism for cholesterol-dependent cytolysins

2019 ◽  
Author(s):  
Shichao Pang ◽  
Junchen Yang ◽  
Jingfang Wang
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Structural Model ◽  
Hydrophobic Interactions ◽  
Free Energy Calculations ◽  
Forming Process ◽  
Hydrophobic Force ◽  
Forming Mechanism ◽  
Hydrophobic Pore ◽  
Dynamics Simulations

ABSTRACTDuring the pore-forming process, cholesterol-dependent cytolysins (CDCs) bind to cholesterol-rich membranes and subsequently undergo a series of conformational changes, predominantly involving in the collapse of the protein and the transformation from α helices to β-hairpins to form a large hydrophobic pore. In the current study, we reconstructed a structural model for both the prepore and pore-forming complexes of PFO based on the cryo-EM data of pneumolysin and performed molecular dynamics simulations and free energy calculations to study the conformational changes in the PFO prepore-to-pore conversion. Our simulations indicate that D2 cannot collapse spontaneously due to the hydrogen bonding and pi-pi interactions between domains D2 and D3, which are partially weakened by binding to cell membranes and oligomerization. The free energy landscape for the prepore-to-pore conversion reveals that an additional force is required for the collapse of D2 to overcome an energy barrier of ∼ 24 kcal/mol. Based on these computational results, we proposed a hydrophobic force-induced pore-forming mechanism to explain the pore-forming process of CDCs. In this mechanism, the hydrophobic interactions between the TMHs and membranes are essential for the prepore-to-pore conversion. The hydrophobic force generated by the TMHs-membrane interactions drives the conformational changes in domains D2 and D3. These findings well explain how the conformational changes within two distant domains synergistically occur, and fits well for the previous biophysical and biochemical data.

scholarly journals Adsorption of Hyperbranched Arabinogalactan-Proteins from Plant Exudate at the Solid–Liquid Interface

2019 ◽  
Vol 3 (2) ◽  
pp. 49 ◽  
Author(s):  
Athénaïs Davantès ◽  
Michaël Nigen ◽  
Christian Sanchez ◽  
Angelina d’Orlando ◽  
Denis Renard
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Gold Surface ◽  
Dry Mass ◽  
Arabinogalactan Proteins ◽  
Liquid Interface ◽  
Gold Substrate ◽  
Solid Liquid Interface ◽  
Solid Liquid

Adsorption of hyperbranched arabinogalactan-proteins (AGPs) from two plant exudates, A. senegal and A. seyal, was thoroughly studied at the solid–liquid interface using quartz crystal microbalance with dissipation monitoring (QCM-D), surface plasmon resonance (SPR), and atomic force microscopy (AFM). Isotherms of the adsorption reveal that 3.3 fold more AGPs from A. seyal (500 ppm) are needed to cover the gold surface compared to A. senegal (150 ppm). The pH and salt concentration of the environment greatly affected the adsorption behavior of both gums, with the surface density ranging from 0.92 to 3.83 mg m−2 using SPR (i.e., “dry” mass) and from 1.16 to 19.07 mg m−2 using QCM-D (wet mass). Surprisingly, the mass adsorbed was the highest in conditions of strong electrostatic repulsions between the gold substrate and AGPs, i.e., pH 7.0, highlighting the contribution of other interactions involved in the adsorption process. Structural changes of AGPs induced by pH would result in swelling of the polysaccharide blocks and conformational changes of the polypeptide backbone, therefore increasing the protein accessibility and hydrophobic interactions and/or hydrogen bonds with the gold substrate.

gp130 activation is regulated by D2–D3 interdomain connectivity

2013 ◽  
Vol 450 (3) ◽  
pp. 487-496 ◽  
Author(s):  
Antje Schütt ◽  
Martin Zacharias ◽  
Nico Schneider ◽  
Silke Horn ◽  
Joachim Grötzinger ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Hepatocellular Adenoma ◽  
Amino Acid Residues ◽  
Hydrophobic Residues ◽  
Binding Epitope ◽  
Interleukin 6 Receptor ◽  
Terminal Amino ◽  
First Time ◽  
Formation Of Complexes

Activation of the IL-6 (interleukin 6) receptor subunit gp130 (glycoprotein 130) has been linked to the formation of complexes with IL-6 and the IL-6 receptor, as well as to gp130 dimerization. However, it has been shown that gp130 is present as a pre-formed dimer, indicating that its activation is not solely dependent on dimerization. Therefore the detailed mechanism of gp130 activation still remains to be deciphered. Recently, deletion mutations of gp130 have been found in inflammatory hepatocellular adenoma. The mutations clustered around one IL-6-binding epitope of gp130 and resulted in a ligand-independent constitutively active gp130. We therefore hypothesized that conformational changes of this particular IL-6-binding epitope precedes gp130 activation. Using a rational structure-based approach we identified for the first time amino acids critical for gp130 activation. We can show that gp130 D2–D3 interdomain connectivity by hydrophobic residues stabilizes inactive gp130 conformation. Conformational destabilization of the EF loop present in domain D2 and disruption of D2–D3 hydrophobic interactions resulted in ligand-independent gp130 activation. Furthermore we show that the N-terminal amino acid residues of domain D1 participate in the activation of the gp130 deletion mutants. Taken together we present novel insights into the molecular basis of the activation of a cytokine receptor signalling subunit.

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