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1
Dubovskii, Peter V., Kira M. Dubova, Gleb Bourenkov, Vladislav G. Starkov, Anastasia G. Konshina, Roman G. Efremov, Yuri N. Utkin, and Valeriya R. Samygina. "Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling." Toxins 14, no. 2 (February 18, 2022): 149. http://dx.doi.org/10.3390/toxins14020149.
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Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from Naja naja cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both “water” and “membrane” conformations of the central loop (loop-2) were determined by X-ray crystallography. The “water” conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The “membrane” conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from N. oxiana (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step—the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their “water” NMR models. We found that the both toxins transform their “water” conformation of loop-2 into the “membrane” one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.
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Greve, Tanja M., Kristine B. Andersen, and Ole F. Nielsen. "Penetration mechanism of dimethyl sulfoxide in human and pig ear skin: An ATR–FTIR and near-FT Raman spectroscopicin vivoandin vitrostudy." Spectroscopy 22, no. 5 (2008): 405–17. http://dx.doi.org/10.1155/2008/109782.
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The penetration mechanism of dimethyl sulfoxide (DMSO) in human skinin vivoandin vitroand pig ear skin in vitro was studied using attenuated total reflectance (ATR) Fourier transform (FT) infrared (IR) and near-FT-Raman spectroscopy. The results showed changes in the conformation of the skin keratins from an α-helical to a β-sheet conformation. These changes were proved to depend on the concentration of free water in the sample as DMSO tended to bind to free water before the protein-bound water was replaced and the protein conformational changes were induced. The induced conformational changes were shown to be completely reversible as the proteins are returned to their original state within 20 h after the treatment with DMSO. The penetration depth of DMSO was shown to depend on the time of exposure – however, after only 15 min DMSO has penetrated thestratum corneum, which is the skin barrier.
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Bridelli, Maria Grazia, and Rosanna Capelletti. "Hydration structure analysis of lysozyme amyloid fibrils by thermally stimulated depolarization currents (TSDC) technique." Spectroscopy 22, no. 2-3 (2008): 165–76. http://dx.doi.org/10.1155/2008/793491.
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Thermally stimulated depolarization currents technique has been employed to investigate the conformation of hen egg white lysozyme in native and amyloid form, in the state of powder at very low hydration level. The technique, able to detect the current generated by thermally activated reorientation of water dipoles previously oriented by an electric field, exploits H2O dipoles, belonging to the solvation shell, as a probe to gain information on the protein conformation.Large differences are detected between the TSDC spectra related to the two different protein conformations, for what concerns the number and position of the main peaks, the native form displaying two peaks, atTM=175 K and atTM=297 K, and the amyloid one, only one at intermediate temperature (TM=235 K). The spectra have been compared with those monitored for poly-L-lysine (MW 80400), as received and prepared in different ways, i.e.α-helix,β-sheet, and coil conformation, respectively. The poly-L-lysine spectra show specific features that can be attributed to water texture around the secondary structure adopted by the macromolecule: the results stress how TSDC technique is a tool of great potential value in the conformational analysis of proteins.
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Dér, A., L. Kelemen, L. Fábián, S. G. Taneva, E. Fodor, T. Páli, A. Cupane, M. G. Cacace, and J. J. Ramsden. "Interfacial Water Structure Controls Protein Conformation." Journal of Physical Chemistry B 111, no. 19 (May 2007): 5344–50. http://dx.doi.org/10.1021/jp066206p.
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Dér, A. "Salts, Interfacial Water and Protein Conformation." Biotechnology & Biotechnological Equipment 22, no. 1 (January 2008): 629–33. http://dx.doi.org/10.1080/13102818.2008.10817524.
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Nagae, Takayuki, Hiroyuki Yamada, and Nobuhisa Watanabe. "High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP+." Acta Crystallographica Section D Structural Biology 74, no. 9 (September 1, 2018): 895–905. http://dx.doi.org/10.1107/s2059798318009397.
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A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP+ and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP+ cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.
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Biedermannová, Lada, and Bohdan Schneider. "Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures." Acta Crystallographica Section D Biological Crystallography 71, no. 11 (October 27, 2015): 2192–202. http://dx.doi.org/10.1107/s1399004715015679.
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Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
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Laugwitz, Jeannette M., Haleh H. Haeri, Anette Kaiser, Ulrike Krug, Dariush Hinderberger, Annette G. Beck-Sickinger, and Peter Schmidt. "Probing the Y2 Receptor on Transmembrane, Intra- and Extra-Cellular Sites for EPR Measurements." Molecules 25, no. 18 (September 10, 2020): 4143. http://dx.doi.org/10.3390/molecules25184143.
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The function of G protein-coupled receptors is intrinsically linked to their conformational dynamics. In conjugation with site-directed spin labeling, electron paramagnetic resonance (EPR) spectroscopy provides powerful tools to study the highly dynamic conformational states of these proteins. Here, we explored positions for nitroxide spin labeling coupled to single cysteines, introduced at transmembrane, intra- and extra-cellular sites of the human neuropeptide Y2 receptor. Receptor mutants were functionally analyzed in cell culture system, expressed in Escherichia coli fermentation with yields of up to 10 mg of purified protein per liter expression medium and functionally reconstituted into a lipid bicelle environment. Successful spin labeling was confirmed by a fluorescence assay and continuous wave EPR measurements. EPR spectra revealed mobile and immobile populations, indicating multiple dynamic conformational states of the receptor. We found that the singly mutated positions by MTSL ((1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl) methyl methanesulfonothioate) have a water exposed immobilized conformation as their main conformation, while in case of the IDSL (bis(1-oxyl-2,2,5,5-tetramethyl-3-imidazolin-4-yl) disulfide) labeled positions, the main conformation are mainly of hydrophobic nature. Further, double cysteine mutants were generated and examined for potential applications of distance measurements by double electron–electron resonance (DEER) pulsed EPR technique on the receptor.
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Maciag, Joseph J., Sarah H. Mackenzie, Matthew B. Tucker, Joshua L. Schipper, Paul Swartz, and A. Clay Clark. "Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection." Proceedings of the National Academy of Sciences 113, no. 41 (September 28, 2016): E6080—E6088. http://dx.doi.org/10.1073/pnas.1603549113.
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The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.
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Martini, Silvia, Claudia Bonechi, Alberto Foletti, and Claudio Rossi. "Water-Protein Interactions: The Secret of Protein Dynamics." Scientific World Journal 2013 (2013): 1–6. http://dx.doi.org/10.1155/2013/138916.
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Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS) and selective (R1SE) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.
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Wang, Chaofan, Na Ji, Lei Dai, Yang Qin, Rui Shi, Liu Xiong, and Qingjie Sun. "The Mechanism Underlying the Amylose-Zein Complexation Process and the Stability of the Molecular Conformation of Amylose-Zein Complexes in Water Based on Molecular Dynamics Simulation." Foods 12, no. 7 (March 27, 2023): 1418. http://dx.doi.org/10.3390/foods12071418.
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The aim of this study was to employ molecular dynamics simulations to elucidate the mechanism involved in amylose–zein complexation and the stability of the molecular conformation of amylose–zein complexes in water at the atomic and molecular levels. The average root mean square deviation and radius of gyration were lower for amylose–zein complexes (1.11 nm and 1 nm, respectively) than for amylose (2.13 nm and 1.2 nm, respectively), suggesting a significantly higher conformational stability for amylose–zein complexes than for amylose in water. The results of radial distribution function, solvent-accessible surface area, and intramolecular and intermolecular hydrogen bonds revealed that the amylose–zein interaction inhibited water permeation into the amylose cavity, leading to enhanced conformational stabilities of the V-type helical structure of amylose and the amylose–zein complexes. Furthermore, the amylose in amylose–zein complexes displayed the thermodynamically stable 4C1 conformation. These findings can provide theoretical guidance in terms of the application of protein on starch processing aiming to improve the physicochemical and functional properties of starch (such as swelling capacity, pasting properties, and digestibility) for developing novel low-digestibility starch–protein products.
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Garcia-Iriepa, Cristina, and Isabelle Navizet. "Effect of Protein Conformation and AMP Protonation State on Fireflies’ Bioluminescent Emission." Molecules 24, no. 8 (April 20, 2019): 1565. http://dx.doi.org/10.3390/molecules24081565.
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The emitted color in fireflies’ bioluminescent systems depends on the beetle species the system is extracted from and on different external factors (pH, temperature…) among others. Controlling the energy of the emitted light (i.e., color) is of crucial interest for the use of such bioluminescent systems. For instance, in the biomedical field, red emitted light is desirable because of its larger tissue penetration and lower energies. In order to investigate the influence of the protein environment and the AMP protonation state on the emitted color, the emission spectra of the phenolate-keto and phenolate-enol oxyluciferin forms have been simulated by means of MD simulations and QM/MM calculations, considering: two different protein conformations (with an open or closed C-terminal domain with respect to the N-terminal) and two protonation states of AMP. The results show that the emission spectra when considering the protein characterized by a closed conformation are blue-shifted compared to the open conformation. Moreover, the complete deprotonation of AMP phosphate group (AMP2−) can also lead to a blue-shift of the emission spectra but only when considering the closed protein conformation (open form is not sensitive to changes of AMP protonation state). These findings can be reasoned by the different interactions (hydrogen-bonds) found between oxyluciferin and the surrounding (protein, AMP and water molecules). This study gets partial insight into the possible origin of the emitted color modulation by changes of the pH or luciferase conformations.
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JÄNIS, Janne, Juha ROUVINEN, Matti LEISOLA, Ossi TURUNEN, and Pirjo VAINIOTALO. "Thermostability of endo-1,4-β-xylanase II from Trichoderma reesei studied by electrospray ionization Fourier-transform ion cyclotron resonance MS, hydrogen/deuterium-exchange reactions and dynamic light scattering." Biochemical Journal 356, no. 2 (May 24, 2001): 453–60. http://dx.doi.org/10.1042/bj3560453.
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Endo-1,4-β-xylanase II (XYNII) from Trichoderma reesei is a 21kDa enzyme that catalyses the hydrolysis of xylan, the major plant hemicellulose. It has various applications in the paper, food and feed industries. Previous thermostability studies have revealed a significant decrease in enzymic activity of the protein at elevated temperatures in citrate buffer [Tenkanen, Puls and Poutanen (1992) Enzyme Microb. Technol. 14, 566–574]. Here, thermostability of XYNII was investigated using both conventional and nanoelectrospray ionization Fourier-transform ion cyclotron resonance MS and hydrogen/deuterium (H/D)-exchange reactions. In addition, dynamic light scattering (DLS) was used as a comparative method to observe possible changes in both tertiary and quaternary structures of the protein. We observed a significant irreversible conformational change and dimerization when the protein was exposed to heat. H/D exchange revealed two distinct monomeric protein populations in a narrow transition temperature region. The conformational change in both the water and buffered solutions occurred in the same temperature region where enzymic-activity loss had previously been observed. Approx. 10–30% of the protein was specifically dimerized when exposed to the heat treatment. However, adding methanol to the solution markedly lowered the transition temperature of conformational change as well as increased the dimerization up to 90%. DLS studies in water confirmed the change in conformation observed by electrospray ionization MS. We propose that the conformational change is responsible for the loss of enzymic activity at temperatures over 50°C and that the functioning of the active site in the enzyme is unfeasible in a new, more labile solution conformation.
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Yao, Hongwei, Michelle W. Lee, Alan J. Waring, Gerard C. L. Wong, and Mei Hong. "Viral fusion protein transmembrane domain adopts β-strand structure to facilitate membrane topological changes for virus–cell fusion." Proceedings of the National Academy of Sciences 112, no. 35 (August 17, 2015): 10926–31. http://dx.doi.org/10.1073/pnas.1501430112.
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The C-terminal transmembrane domain (TMD) of viral fusion proteins such as HIV gp41 and influenza hemagglutinin (HA) is traditionally viewed as a passive α-helical anchor of the protein to the virus envelope during its merger with the cell membrane. The conformation, dynamics, and lipid interaction of these fusion protein TMDs have so far eluded high-resolution structure characterization because of their highly hydrophobic nature. Using magic-angle-spinning solid-state NMR spectroscopy, we show that the TMD of the parainfluenza virus 5 (PIV5) fusion protein adopts lipid-dependent conformations and interactions with the membrane and water. In phosphatidylcholine (PC) and phosphatidylglycerol (PG) membranes, the TMD is predominantly α-helical, but in phosphatidylethanolamine (PE) membranes, the TMD changes significantly to the β-strand conformation. Measured order parameters indicate that the strand segments are immobilized and thus oligomerized. 31P NMR spectra and small-angle X-ray scattering (SAXS) data show that this β-strand–rich conformation converts the PE membrane to a bicontinuous cubic phase, which is rich in negative Gaussian curvature that is characteristic of hemifusion intermediates and fusion pores. 1H-31P 2D correlation spectra and 2H spectra show that the PE membrane with or without the TMD is much less hydrated than PC and PG membranes, suggesting that the TMD works with the natural dehydration tendency of PE to facilitate membrane merger. These results suggest a new viral-fusion model in which the TMD actively promotes membrane topological changes during fusion using the β-strand as the fusogenic conformation.
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Sanchez-Fernandez, A., K. J. Edler, T. Arnold, D. Alba Venero, and A. J. Jackson. "Protein conformation in pure and hydrated deep eutectic solvents." Physical Chemistry Chemical Physics 19, no. 13 (2017): 8667–70. http://dx.doi.org/10.1039/c7cp00459a.
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Bingle, Wade H., James L. Doran, and William J. Page. "Characterization of the surface layer protein from Azotobacter vinelandii." Canadian Journal of Microbiology 32, no. 2 (February 1, 1986): 112–20. http://dx.doi.org/10.1139/m86-023.
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The regular surface array protein (S protein) of Azotobacter vinelandii was extracted from outer membrane fragments with distilled water and further purified by gel filtration chromatography. The protein was shown to behave anomalously on sodium dodecyl sulfate polyacrylamide gels producing a number of conformational isomers. The amino acid composition of S protein was similar to that of other surface array proteins, particularly in its lack of cysteine. The theoretical monomelic molecular weight of S protein was calculated to be 60 218 based on the total amino acid composition and the apparent molecular weight determined by sodium dodecyl sulfate – polyacrylamide gel electrophoresis. Circular dichroism spectra indicated that S protein was composed of approximately 35% β sheet structure, negligible α helix, with the remainder of the polypeptide backbone aperiodic in nature. The effect of the divalent cations Ca2+ and Mg2+ on the conformation of S protein was examined by circular dichroism spectroscopy; however, no conformational change was detected in response to the presence of these species nor did S-protein monomer aggregate into multimers in the presence of these cations. Purified S-protein monomer was inactive in divalent cation mediated reassembly of the S layer onto the surface of distilled water washed cells. A larger multimeric form present only in fresh preparations appeared to be the active species involved in in vitro reassembly of the A. vinelandii surface array.
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Kar, L., P. Matsumura, and M. E. Johnson. "Bivalent-metal binding to CheY protein. Effect on protein conformation." Biochemical Journal 287, no. 2 (October 15, 1992): 521–31. http://dx.doi.org/10.1042/bj2870521.
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CheY is a 14 kDa cytoplasmic protein that is activated by the transfer of a phosphoryl moiety to Asp-57 from phosphoCheA during signal transduction in bacterial chemotaxis. It has been established that metal ions are necessary for the autophosphorylation of CheA, the transfer of phosphate from phosphoCheA to CheY and the autodephosphorylation of phosphoCheY. In this work, paramagnetic relaxation enhancement has been used in conjunction with one- and two-dimensional n.m.r. to study the interaction of CheY with bivalent metal ions. These studies have led to the discovery of two conformations of the protein in water, corresponding to the metal-free and the metal-bound states. Binding of bivalent cations like Mg2+, Ca2+, Sr2+, Zn2+ and Mn2+ results in a conformational change from the metal-free to the metal-bound state. Preliminary assignments of the aromatic proton resonances are reported. Comparison of phase-sensitive double-quantum-filtered COSY, homonuclear Hartmann-Hahn coherence transfer and nuclear Overhauser enhancement spectra from the metal-bound and metal-free protein indicates that Trp-58, Thr-87 and Tyr-106 are particularly affected by the conformational change involved, and that this change is limited to a small number of residues. In addition, homonuclear Hartmann-Hahn coherence transfer experiments with paramagnetic Mn2+ show significant suppression of cross-peaks associated with Trp-58 and several neighbouring residues. Comparison of the distances estimated using n.m.r. with the CheY crystal structure indicates that the n.m.r. results are consistent with bivalent metal binding at the cluster of aspartic acid residues that includes Asp-13 and Asp-57. These studies also demonstrate the utility of paramagnetic metal-induced relaxation in conjunction with two-dimensional n.m.r. measurements for exploring ligand-binding sites.
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Tatham, A. S., A. F. Drake, and P. R. Shewry. "Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein." Biochemical Journal 259, no. 2 (April 15, 1989): 471–76. http://dx.doi.org/10.1042/bj2590471.
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C hordein, a storage protein from barley grains, has an Mr of about 53,000, and consists predominantly of repeated octapeptides with a consensus sequence of Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln. Previously reported hydrodynamic and c.d. studies indicate the presence of beta-turns, the repetitive nature of which may lead to the formation of a loose spiral. In order to study these turns we have compared the structures of a synthetic peptide corresponding to the consensus repeat motif and total C hordein by using c.d. and Fourier-transform i.r. spectroscopy. The synthetic peptide exhibited spectra typical of beta I/III reverse turns when dissolved in trifluoroethanol at 22 degrees C and in water at 70 degrees C, but ‘random-coil’-like spectra in water at 22 degrees C. The whole protein also showed increases in beta I/III reverse turns when dissolved in increasing concentrations of trifluoroethanol (50-100%, v/v) or heated in ethanol/water (7:3, v/v). Two cryogenic solvent systems were used to determine the c.d. spectra of the peptide and protein at temperatures down to -100 degrees C. Methanol/glycerol (9:1, v/v) and ethanediol/water (2:1, v/v) were selected as analogues of trifluoroethanol/water and water respectively. The peptide exhibited beta I/III-reverse-turn and ‘random-coil’-like spectra in methanol/glycerol and ethanediol/water respectively at 22 degrees C, but a spectrum similar to that of a poly-L-proline II helix in both solvents at -100 degrees C. Similarly the proportion of this spectral type also increased when the whole protein was cooled in both solvents. These results indicate that a poly-L-proline II conformation at low temperatures is in equilibrium with a beta I/III-turn-rich conformation at higher temperatures. The latter conformation is also favoured in solvents of low dielectric constant such as trifluoroethanol. The ‘random-coil‘-like spectra exhibited by the protein and peptide in high-dielectric-constant solvents at room temperature may result from a mixture of the two conformations rather than from the random-coil state.
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Rand, R. P. "Probing the role of water in protein conformation and function." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1448 (August 29, 2004): 1277–85. http://dx.doi.org/10.1098/rstb.2004.1504.
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Life began in a bath of water and has never escaped it. Cellular function has forced the evolution of many mechanisms ensuring that cellular water concentration has never changed significantly. To free oneself of any conceptual distinction among all small molecules, solutes and solvents, means that experiments to probe water's specific role in molecular function can be designed like any classical chemical reaction. Such an ‘osmotic stress’ strategy will be described in general and for an enzyme, hexokinase. Water behaves like a reactant that competes with glucose in binding to hexokinase, and modulates its conformational change and activity. This ‘osmotic stress’ strategy, now applied to many very different systems, shows that water plays a significant role, energetically, in most macromolecular reactions. It can be required to fill obligatory space, it dominates nearest non–specific interactions between large surfaces, it can be a reactant modulating conformational change; all this in addition to its more commonly perceived static role as an integral part of stereospecific intramolecular structure.
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BYRNE, NOLENE, COLIN BARROW, and ADAM MCCLUSKEY. "SOLVENT INDUCED CHANGES IN THE CONFORMATIONAL STATE OF β-LACTOGLOBULIN AND THE INFLUENCE OF PROTIC IONIC LIQUIDS." Journal of Molecular and Engineering Materials 01, no. 01 (January 2013): 1250004. http://dx.doi.org/10.1142/s2251237312500049.
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The protic ionic liquids (pILs), triethylammonium acetate, triethylammonium trifluoroacetate, triethylammonium mesylate and trimethylammonium sulfate were used to induce various native and non-native conformational states of the protein β-lactoglobulin (βLG). Changes in the secondary structure of βLG were observed on moving from a high water content to a high pIL content. We examined the stability of various pIL induced states via thermal unfolding and refolding, where it was found that at a given pIL concentration a highly stable non-native conformation was formed. The βLG non-native conformation was characterized by a high α-helical content. Additionally, pIL conditions that promoted amyloid fibril formation were identified and characterized by CD, a Thioflavin T binding assay and transmission electron microscopy (TEM). This work highlights the use of pILs as solvents in the study of protein folding using βLG as a model system.
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Nam, Ki Hyun. "Crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid." Acta Crystallographica Section D Structural Biology 77, no. 7 (June 29, 2021): 954–65. http://dx.doi.org/10.1107/s2059798321005763.
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The brain-type fatty acid-binding protein FABP7, which is expressed in astrocytes and neural progenitors, is a member of the intracellular lipid-binding protein family. This protein is not only involved in various cellular functions such as metabolism, inflammation and energy homeostasis, but also in diseases such as cognitive disorders and tumors. Structures of unsaturated fatty acids, such as oleic acid (OA) and docosahexaenoic acid (DHA), bound to FABP7 have been elucidated; however, structures of saturated fatty acids bound to FABP7 remain unknown. To better understand fatty acid recognition, here the crystal structure of human brain-type fatty acid-binding protein FABP7 complexed with palmitic acid (PA), a saturated fatty acid, is reported at a resolution of 1.6 Å. The PA bound to the fatty acid-binding pocket of FABP7 assumed a U-shaped conformation. The carboxylate moiety of PA interacted with Tyr129, Arg127 and, via a water bridge, with Arg107 and Thr54, whereas its aliphatic chain was stabilized by hydrophobic interactions with Met21, Leu24, Thr30, Thr37, Pro39, Phe58 and Asp77. Structural comparison showed that PA, OA and DHA exhibited unique binding conformations in the fatty acid-binding pocket, stabilized by distinct amino-acid interactions. The binding of PA to FABP7 exhibits a unique binding conformation when compared with other human FABPs (FABP3–FABP5 and FABP8) expressed in other tissues. Based on the crystal and fatty acid structures, it was suggested that PA, which prefers a linear form in nature, required a greater conformational change in its aliphatic chain to bind to the fatty acid-binding pocket in a U-shaped conformation, compared with the cis configurations of OA or DHA. This, together with the length of the aliphatic chain, was considered to be one of the factors determining the binding affinity of PA to FABP7. These results provide a better understanding of fatty acid recognition by FABP7 and expand the knowledge of the binding of PA to FABPs.
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Levine, Zachary A., Luca Larini, Nichole E. LaPointe, Stuart C. Feinstein, and Joan-Emma Shea. "Regulation and aggregation of intrinsically disordered peptides." Proceedings of the National Academy of Sciences 112, no. 9 (February 17, 2015): 2758–63. http://dx.doi.org/10.1073/pnas.1418155112.
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Intrinsically disordered proteins (IDPs) are a unique class of proteins that have no stable native structure, a feature that allows them to adopt a wide variety of extended and compact conformations that facilitate a large number of vital physiological functions. One of the most well-known IDPs is the microtubule-associated tau protein, which regulates microtubule growth in the nervous system. However, dysfunctions in tau can lead to tau oligomerization, fibril formation, and neurodegenerative disease, including Alzheimer’s disease. Using a combination of simulations and experiments, we explore the role of osmolytes in regulating the conformation and aggregation propensities of the R2/wt peptide, a fragment of tau containing the aggregating paired helical filament (PHF6*). We show that the osmolytes urea and trimethylamine N-oxide (TMAO) shift the population of IDP monomer structures, but that no new conformational ensembles emerge. Although urea halts aggregation, TMAO promotes the formation of compact oligomers (including helical oligomers) through a newly proposed mechanism of redistribution of water around the perimeter of the peptide. We put forth a “superposition of ensembles” hypothesis to rationalize the mechanism by which IDP structure and aggregation is regulated in the cell.
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Chinnathambi, Shanmugavel, Nobutaka Hanagata, Tomohiko Yamazaki, and Naoto Shirahata. "Nano-Bio Interaction between Blood Plasma Proteins and Water-Soluble Silicon Quantum Dots with Enabled Cellular Uptake and Minimal Cytotoxicity." Nanomaterials 10, no. 11 (November 13, 2020): 2250. http://dx.doi.org/10.3390/nano10112250.
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A better understanding of the compatibility of water-soluble semiconductor quantum dots (QDs) upon contact with the bloodstream is important for biological applications, including biomarkers working in the first therapeutic spectral window for deep tissue imaging. Herein, we investigated the conformational changes of blood plasma proteins during the interaction with near-infrared light-emitting nanoparticles, consisting of Pluronic F127 shells and cores comprised of assembled silicon QDs terminated with decane monolayers. Albumin and transferrin have high quenching constants and form a hard protein corona on the nanoparticle. In contrast, fibrinogen has low quenching constants and forms a soft protein corona. A circular dichroism (CD) spectrometric study investigates changes in the protein’s secondary and tertiary structures with incremental changes in the nanoparticle concentrations. As expected, the addition of nanoparticles causes the denaturation of the plasma proteins. However, it is noteworthy that the conformational recovery phenomena are observed for fibrinogen and transferrin, suggesting that the nanoparticle does not influence the ordered structure of proteins in the bloodstream. In addition, we observed enabled cellular uptake (NIH3T3 Fibroblasts) and minimal cytotoxicity using different cell lines (HeLa, A549, and NIH3T3). This study offers a basis to design QDs without altering the biomacromolecule’s original conformation with enabled cellular uptake with minimal cytotoxicity.
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Wang, Xixi, Jiankai Shan, Wei Liu, Jing Li, Hongwei Tan, Xichen Li, and Guangju Chen. "Theoretical Studies on the Binding Mode and Reaction Mechanism of TLP Hydrolase kpHIUH." Molecules 26, no. 13 (June 25, 2021): 3884. http://dx.doi.org/10.3390/molecules26133884.
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In this work, we have investigated the binding conformations of the substrate in the active site of 5-HIU hydrolase kpHIUH and its catalytic hydrolysis mechanism. Docking calculations revealed that the substrate adopts a conformation in the active site with its molecular plane laying parallel to the binding interface of the protein dimer of kpHIUH, in which His7 and His92 are located adjacent to the hydrolysis site C6 and have hydrogen bond interactions with the lytic water. Based on this binding conformation, density functional theory calculations indicated that the optimal catalytic mechanism consists of two stages: (1) the lytic water molecule is deprotonated by His92 and carries out nucleophilic attack on C6=O of 5-HIU, resulting in an oxyanion intermediate; (2) by accepting a proton transferred from His92, C6–N5 bond is cleaved to completes the catalytic cycle. The roles of His7, His92, Ser108 and Arg49 in the catalytic reaction were revealed and discussed in detail.
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SU, XIAODI. "SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY." COSMOS 05, no. 01 (May 2009): 79–95. http://dx.doi.org/10.1142/s0219607709000415.
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Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformational changes in the proteins and DNA. These are all important characteristics underlining the mechanism of ER-mediated gene transcription. With these studies we have made the following demonstrations to describe the advantages of these two techniques, namely (i) SPR technique is superior and more versatile than conventional (electrophoretic mobility shift assay) EMSA for studying protein-DNA interactions; (ii) QCM is an alternative tool for studying conformational changes in protein–DNA complexes and (iii) combinational SPR and QCM analysis provides additional characterization of biomolecular films, e.g. film thickness, water content, and conformation rigidity etc.
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Palm, Daniel M., Alessandro Agostini, Anne-Christin Pohland, Mara Werwie, Elmar Jaenicke, and Harald Paulsen. "Stability of Water-Soluble Chlorophyll Protein (WSCP) Depends on Phytyl Conformation." ACS Omega 4, no. 5 (May 2019): 7971–79. http://dx.doi.org/10.1021/acsomega.9b00054.
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Qiao, Baofu, Felipe Jiménez-Ángeles, Trung Dac Nguyen, and Monica Olvera de la Cruz. "Water follows polar and nonpolar protein surface domains." Proceedings of the National Academy of Sciences 116, no. 39 (September 9, 2019): 19274–81. http://dx.doi.org/10.1073/pnas.1910225116.
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The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.
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Esposito, Luciana, Nicole Balasco, Alfonso De Simone, Rita Berisio, and Luigi Vitagliano. "Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts." BioMed Research International 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/326914.
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Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-Cα-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-Cα-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral anglesΔω/ψin collagen-like models may have interesting implications for triple helix stability.
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Cameron, Ivan L., and Gary D. Fullerton. "A model to explain the osmotic pressure behavior of hemoglobin and serum albumin." Biochemistry and Cell Biology 68, no. 5 (May 1, 1990): 894–98. http://dx.doi.org/10.1139/o90-132.
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Previously published osmotic pressure data on hemoglobin and bovine serum albumin were used to determine the osmotically unresponsive solvent volume per unit dry mass of protein. A model is presented that accounts for the osmotic pressure of globular proteins based on a surface-associated osmotically unresponsive solvent volume. The model also accounts for changes in the osmotically unresponsive solvent volume owing to changes in pH, cosolute salt concentration, protein conformation, and protein aggregation.Key words: hemoglobin, serum albumin, osmotic pressure, water of hydration, salt, pH, model of protein structure.
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Xiao, Naidong, Yinguang Chen, and Hongqiang Ren. "Altering protein conformation to improve fermentative hydrogen production from protein wastewater." Water Research 47, no. 15 (October 2013): 5700–5707. http://dx.doi.org/10.1016/j.watres.2013.06.047.
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Viljoen, C., C. J. R. Verbeek, and K. L. Pickering. "The Use of Aqueous Urea as Chemical Denaturant in Processing CGM into a Biodegradable Polymer Material." Advanced Materials Research 29-30 (November 2007): 181–84. http://dx.doi.org/10.4028/www.scientific.net/amr.29-30.181.
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Corn gluten meal (CGM) has potential as a bioderived polymer for use in composite materials. Previous work to improve the processability of CGM has focused on the use of plasticisers including water, polyethylene glycol, glycerol and octanoic acid, however, a common problem is that these leach from the material subsequent to processing [1]. It has been raised that a certain degree of denaturation must occur in order to make proteins processable [2]. The current work explores the use of aqueous urea as chemical denaturant in processing CGM into a biodegradable polymer material. Consolidated materials were obtained which showed increased resistance to cracking with higher urea concentration. FTIR analysis revealed that processing CGM with increased concentrations of aqueous urea resulted in the progressive transformation of the protein secondary structure from an ordered, clustered conformation to that of extended chains. Aqueous urea is assumed to promote protein-solvent interactions which stabilise the extended chain conformations.
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Law, Peter B., and Valerie Daggett. "The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures." Protein Engineering, Design and Selection 23, no. 1 (November 16, 2009): 27–33. http://dx.doi.org/10.1093/protein/gzp069.
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Ohkawa, Kousaku, Masakazu Hachisu, Takaomi Nomura, Ryoichi Arai, Kimio Hirabayashi, Masuhiro Tsukada, and Koji Abe. "Chain Conformational Study on Underwater Silk Proteins from Caddisfly, Stenopsyche marmorata - Implication of a Fiber-Forming Mechanism." Advanced Materials Research 796 (September 2013): 3–8. http://dx.doi.org/10.4028/www.scientific.net/amr.796.3.
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Larval silk/cement proteins from a caddisfly, Stenopsyche marmorata, were isolated as a protein mixture of Smsp-1, 2, 3 and 4. Smsp-1 is a giant phosphorylated protein, which occupies ca. 45%-mass of the silk gland content, and composed of a long-range periodic amino acid sequences, involving 8 kinds of characteristic segments. The silk protein film was prepared and drawn in water up to 9-folds of the initial axis length, then the drawn film was subjected to polarized FT-IR and WAXD. The results implied that the Smsp-1 backbone adopts two different conformations, one of which was the β-turn-like conformers. The molecular mechanic studies were separately performed to evaluate the solid-state chain structures of the hydrophobic/Pro-rich segments 3 and 4, which are enriched in the primary sequence of Smsp-1, and the results were coincident with those from the vibration spectra and WAXD. The molecular dynamic (MD) studies were also carried out in order to estimate their preferred chain conformations in a solution state. The MD trajectory suggests that the segments 3 and 4 tend to adopt a turn-like conformation, which is a potential precursor of the β-turn-like conformers. In conclusion, the underwater silk proteins have a fiber-forming mechanism, which is substantially different from a silkworm, Bombyx mori.
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WANG, Shao-Xiong, Yu-Tong SUN, and Sen-Fang SUI. "Membrane-induced conformational change in human apolipoprotein H." Biochemical Journal 348, no. 1 (May 9, 2000): 103–6. http://dx.doi.org/10.1042/bj3480103.
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The interaction of apolipoprotein H (Apo H) with lipid membrane has been considered to be a basic mechanism for the biological function of the protein. Previous reports have demonstrated that Apo H can interact only with membranes containing anionic phospholipids. Here we study the membrane-induced conformational change of Apo H by CD spectroscopy with two different model systems: anionic-phospholipid-containing liposomes [such as 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) and cardiolipin], and the water/methanol mixtures at moderately low pH, which mimic the micro-physicochemical environment near the membrane surface. It is found that Apo H undergoes a remarkable conformational change on interaction with liposomes containing anionic phospholipid. To interact with liposomes containing DMPG, there is a 6.8% increase in α-helix in the secondary structures; in liposomes containing cardiolipin, however, there is a 12.6% increase in α-helix and a 9% decrease in β-sheet. The similar conformation change in Apo H can be induced by treatment with an appropriate mixture of water/methanol. The results indicate that the association of Apo H with membrane is correlated with a certain conformational change in the secondary structure of the protein.
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Pyne, Partha, Debasish Das Mahanta, Himanshu Gohil, S. S. Prabhu, and Rajib Kumar Mitra. "Correlating solvation with conformational pathways of proteins in alcohol–water mixtures: a THz spectroscopic insight." Physical Chemistry Chemical Physics 23, no. 32 (2021): 17536–44. http://dx.doi.org/10.1039/d1cp01841h.
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Nick Pace, C., Saul Treviño, Erode Prabhakaran, and J. Martin Scholtz. "Protein structure, stability and solubility in water and other solvents." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1448 (August 29, 2004): 1225–35. http://dx.doi.org/10.1098/rstb.2004.1500.
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Proteins carry out the most difficult tasks in living cells. They do so by interacting specifically with other molecules. This requires that they fold to a unique, globular conformation that is only marginally more stable than the large ensemble of unfolded states. The folded state is stabilized mainly by the burial and tight packing of over 80% of the peptide groups and non–polar side chains. If life as we know it is to exist in a solvent other than water, the folded state must be stable and soluble in the new solvent. Our analysis suggests that proteins will be unstable in most polar solvents such as ethanol, extremely stable in non–polar solvents such as cyclohexane, and even more stable in a vacuum. Our solubility studies suggest that protein solubility will be markedly lower in polar solvents such as ethanol and that proteins will be essentially insoluble in non–polar solvents such as cyclohexane. For these and other reasons it seems unlikely that the life we know could exist in any solvent system other than water.
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Ou, Wen-bin, Ri-Sheng Wang, and Hai-Meng Zhou. "Conformational changes and inactivation of rabbit muscle creatine kinase in dimethyl sulfoxide solutions." Biochemistry and Cell Biology 80, no. 4 (August 1, 2002): 427–34. http://dx.doi.org/10.1139/o02-132.
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The effects of dimethyl sulfoxide (DMSO) on creatine kinase (CK) conformation and enzymatic activity were studied by measuring activity changes, aggregation, and fluorescence spectra. The results showed that at low concentrations (<65% v/v), DMSO had little effect on CK activity and structure. However, higher concentrations of DMSO led to CK inactivation, partial unfolding, and exposure of hydrophobic surfaces and thiol groups. DMSO caused aggregation during CK denaturation. A 75% DMSO concentration induced the most significant aggregation of CK. The CK inactivation and unfolding kinetics were single phase. The unfolding of CK was an irreversible process in the DMSO solutions. The results suggest that to a certain extent, an enzyme can maintain catalytic activity and conformation in waterorganic mixture environments. Higher concentrations of DMSO affected the enzyme structure but not its active site. Inactivation occurred along with noticeable conformational change during CK denaturation. The inactivation and unfolding of CK in DMSO solutions differed from other denaturants such as guanidine, urea, and sodium dodecyl sulfate. The exposure of hydrophobic surfaces was a primary reason for the protein aggregation.Key words: creatine kinase, dimethyl sulfoxide, denaturation, activity, conformation.
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KHAIRUDIN, NURUL BAHIYAH AHMAD, and HABIBAH A. WAHAB. "PROTEIN STRUCTURE PREDICTION USING GAS PHASE MOLECULAR DYNAMICS SIMULATION: EOTAXIN-3 CYTOKINE AS A CASE STUDY." International Journal of Modern Physics: Conference Series 09 (January 2012): 193–98. http://dx.doi.org/10.1142/s2010194512005259.
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In the current work, the structure of the enzyme CC chemokine eotaxin-3 (1G2S) was chosen as a case study to investigate the effects of gas phase on the predicted protein conformation using molecular dynamics simulation. Generally, simulating proteins in the gas phase tend to suffer from various drawbacks, among which excessive numbers of protein-protein hydrogen bonds. However, current results showed that the effects of gas phase simulation on 1G2S did not amplify the protein-protein hydrogen bonds. It was also found that some of the hydrogen bonds which were crucial in maintaining the secondary structural elements were disrupted. The predicted models showed high values of RMSD, 11.5 Å and 13.5 Å for both vacuum and explicit solvent simulations, respectively, indicating that the conformers were very much different from the native conformation. Even though the RMSD value for the in vacuo model was slightly lower, it somehow suffered from lower fraction of native contacts, poor hydrogen bonding networks and fewer occurrences of secondary structural elements compared to the solvated model. This finding supports the notion that water plays a dominant role in guiding the protein to fold along the correct path.
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Mazela, B., and I. Polus-Ratajczak. "Use of Animal Proteins to Limit Leaching of Active Copper Ions Preservatives from Treated Wood." Holzforschung 57, no. 6 (October 30, 2003): 593–96. http://dx.doi.org/10.1515/hf.2003.089.
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Summary The concept of animal protein utilization aiming to reduce leaching of treatment salts from wood was tested and verified. Animal proteins in the form of spray-dried animal blood plasma were used as an addition to the water solution of fungicidal salt or included in the solution for soaking pre-treated wood. The wood was subjected to thermal treatment which caused protein denaturation, a process which changes the proteins' spatial conformation and reduces their solubility in water. Scots pine wood (Pinus sylvestris L.) was treated with a water solution of copper sulfate using vacuum, vacuum-soaking and vacuum-pressure methods. The animal proteins were added to the treatment solutions or applied by soaking to samples pre-treated with the salt. After treatment, the samples were heated to 100°C. After suitable conditioning, the wood was subjected to leaching. The content of Cu2+ in the water extracts was determined by Atomic Absorption Spectrophotometry (AAS).
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Rao, Wei, M. S. Roopesh, Daodong Pan, and Lihui Du. "Enhanced Gel Properties of Duck Myofibrillar Protein by Plasma-Activated Water: Through Mild Structure Modifications." Foods 12, no. 4 (February 18, 2023): 877. http://dx.doi.org/10.3390/foods12040877.
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This study assessed the gel properties and conformational changes of duck myofibrillar protein (DMP) affected by plasma-activated water (PAW) generated at various discharge times (0 s, 10 s, 20 s, 30 s, and 40 s). With the treatment of PAW-20 s, the gel strength and water-holding capacity (WHC) of DMP gels were significantly increased when compared to the control group. Throughout the heating process, dynamic rheology revealed that the PAW-treated DMP had a higher storage modulus than the control. The hydrophobic interactions between protein molecules were significantly improved by PAW, resulting in a more ordered and homogeneous gel microstructure. The increased sulfhydryl and carbonyl content in DMP indicated a higher degree of protein oxidation with PAW treatment. Additionally, the circular dichroism spectroscopy demonstrated that PAW induced α-helix and β-turn transformed to β-sheet in DMP. Surface hydrophobicity, fluorescence spectroscopy, and UV absorption spectroscopy suggested that PAW altered DMP’s tertiary structure, although the electrophoretic pattern indicated that the primary structure of DMP was mostly unaffected. These results suggest that PAW can improve the gel properties of DMP through mild alteration in its conformation.
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Somers, Kieran P., and David L. Cheung. "The Amyloidogenic Peptide Amyloid Beta(16–22) Displays Facet Dependent Conformation on Metal Surfaces." Biophysica 2, no. 2 (June 9, 2022): 135–53. http://dx.doi.org/10.3390/biophysica2020015.
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Currently, it is not understood how metal nanoparticles influence the formation of protein fibrils, although recent literature highlights that the shape and chemical composition of such nanoparticles can strongly influence the process. Understanding this process at a fundamental level can potentially unlock routes to the development of new therapeutics, as well as novel materials for technological applications. This requires a microscopic picture of the behaviour of amyloidogenic proteins on metal surfaces. Using replica exchange molecular dynamics simulations, we investigate the conformation of the model amyloidogenic peptide, Aβ(16–22), on different gold and silver surfaces. The conformation of the peptide on gold surfaces also shows a strong facet dependence, with fibril-like conformations being promoted in the 100 surface and inhibited on the 111 surface. A smaller degree of facet dependence is seen for silver with the peptide behaving similar on both of these. The difference in the facet dependence can be related to the difference between direct adsorption onto the gold 111 surface, with a preference towards indirect (water mediated) adsorption onto the other surfaces. This new information on the behaviour of an amyloidogenic peptide on metal surfaces can give insight into the size-dependent effect of nanoparticles on fibril formation and the use of surfaces to control fibrillation.
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Seok, Seung-Hyeon, Hookang Im, Hyung-Sik Won, Min-Duk Seo, Yoo-Sup Lee, Hye-Jin Yoon, Min-Jeong Cha, Jin-Young Park, and Bong-Jin Lee. "Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers." Acta Crystallographica Section D Biological Crystallography 70, no. 6 (May 30, 2014): 1726–42. http://dx.doi.org/10.1107/s139900471400724x.
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The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP–CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in asynconformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
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Fisette, Olivier, Gunnar F. Schröder, and Lars V. Schäfer. "Atomistic structure and dynamics of the human MHC-I peptide-loading complex." Proceedings of the National Academy of Sciences 117, no. 34 (August 11, 2020): 20597–606. http://dx.doi.org/10.1073/pnas.2004445117.
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The major histocompatibility complex class-I (MHC-I) peptide-loading complex (PLC) is a cornerstone of the human adaptive immune system, being responsible for processing antigens that allow killer T cells to distinguish between healthy and compromised cells. Based on a recent low-resolution cryo-electron microscopy (cryo-EM) structure of this large membrane-bound protein complex, we report an atomistic model of the PLC and study its conformational dynamics on the multimicrosecond time scale using all-atom molecular dynamics (MD) simulations in an explicit lipid bilayer and water environment (1.6 million atoms in total). The PLC has a layered structure, with two editing modules forming a flexible protein belt surrounding a stable, catalytically active core. Tapasin plays a central role in the PLC, stabilizing the MHC-I binding groove in a conformation reminiscent of antigen-loaded MHC-I. The MHC-I–linked glycan steers a tapasin loop involved in peptide editing toward the binding groove. Tapasin conformational dynamics are also affected by calreticulin through a conformational selection mechanism that facilitates MHC-I recruitment into the complex.
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Pandey, Bharati, Chetna Tyagi, Gopal Kumar Prajapati, Awdhesh Kumar Mishra, Abeer Hashem, Abdulaziz A. Alqarawi, Elsayed Fathi Abd_Allah, and Tapan Kumar Mohanta. "Analysis of mutations of defensin protein using accelerated molecular dynamics simulations." PLOS ONE 15, no. 11 (November 30, 2020): e0241679. http://dx.doi.org/10.1371/journal.pone.0241679.
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Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein 2 (RsAFP2). Accelerated Molecular Dynamics (aMD) were carried out to examine the conformational changes present in these RsAFP2 mutants, and its two closest homologs compared to the wild-type protein. Specifically, the root mean square fluctuation values for the eight cysteine amino acids involved in the four disulfide bonds were low in the V39R mutant compared to the wild-type. Additionally, analysis of the free energy change revealed that G9R and V39R mutations exert a neutral and stabilizing effect on RsAFP2 conformation, and this is supported by the observed lower total energy of mutants compared to the wild-type, suggesting that enhanced stability of the mutants. However, MD simulations to a longer time scale would aid in capturing more conformational state of the wild-type and mutants defensin protein. Furthermore, the aMD simulations on fungal mimic membranes with RsAFP2 and its mutants and homologs showed that the mutant proteins caused higher deformation and water diffusion than the native RsAFP2, especially the V39R mutant. The mutant variants seem to interact by specifically targeting the POPC and POPI lipids amongst others. This work highlights the stabilizing effect of mutations at the 9th and 39th positions of RsAFP2 and their increased membrane deformation activity.
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Kornblatt, Jack A., Tanya A. Barretto, Ketevan Chigogidze, and Bahati Chirwa. "Canine Plasminogen: Spectral Responses to Changes in 6-Aminohexanoate and Temperature." Analytical Chemistry Insights 2 (January 2007): 117739010700200. http://dx.doi.org/10.4137/117739010700200009.
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We studied the near UV absorption spectrum of canine plasminogen. There are 19 tryptophans, 19 phenylalanines and 34 tyrosines in the protein. 4th derivative spectra optimized for either tryptophan or tyrosine give a measure of the polarity of the environments of these two aromatic amino acids. Plasminogen at temperatures between 0°C and 37°C exists as a mixture of four conformations: closed-relaxed, open-relaxed, closed-compact, and open-compact. The closed to open transition is driven by addition of ligand to a site on the protein. The relaxed to compact transition is driven by increasing temperature from 0°C to above 15-20°C. When the conformation of plasminogen is mainly closed-relaxed, the 4th derivative spectra suggest that the average tryptophan environment is similar to a solution of 20% methanol at the same temperature. Under the same conditions, 4th derivative spectra suggest that the average tyrosine environment is similar to water. These apparent polarities change as the plasminogen is forced to assume the other conformations. We try to rationalize the information based on the known portions of the plasminogen structure.
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Guo, Liping, Xuecong Zhang, Lin Xu, Yan Li, Bin Pang, Jingxin Sun, Baowei Wang, Ming Huang, Xinglian Xu, and Harvey Ho. "Efficacy and Mechanism of Ultrasound Combined with Slightly Acidic Electrolyzed Water for Inactivating Escherichia coli." Journal of Food Quality 2021 (March 9, 2021): 1–10. http://dx.doi.org/10.1155/2021/6689751.
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In the present study, the synergetic effect and mechanism of ultrasound (US) and slightly acidic electrolyzed water (SAEW) on the inactivation of Escherichia coli (E. coli) were evaluated. The results showed that US combined with SAEW treatment showed higher sanitizing efficacy for reducing E. coli than US and SAEW alone treatment. US and US combined with SAEW treatments resulted in smaller particle size of E. coli compared to the control and SAEW treatment. In addition, US combined with SAEW treatment induced the highest potassium leakage. However, the highest protein leakage was recorded in US treatment. Moreover, scanning and transmission electron microscopy analysis revealed that the greatest damage of the appearance and ultrastructure of E. coli was achieved after US combined with SAEW treatment. The synergetic effect was also confirmed by CLSM analysis. Fluorescence spectroscopy suggested that treatments of US, SAEW, and US combined with SAEW changed protein conformation of E. coli. Overall, the present study demonstrated that the sterilization mechanism of US combined with SAEW treatment was decreasing the particle size and disrupting the permeability of cell membrane and the cytoplasmic ultrastructure as well as changing protein conformation of E. coli.
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Vermaas, Josh V., Susan B. Rempe, and Emad Tajkhorshid. "Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE." Proceedings of the National Academy of Sciences 115, no. 32 (July 19, 2018): E7502—E7511. http://dx.doi.org/10.1073/pnas.1722399115.
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EmrE is a small, homodimeric membrane transporter that exploits the established electrochemical proton gradient across the Escherichia coli inner membrane to export toxic polyaromatic cations, prototypical of the wider small-multidrug resistance transporter family. While prior studies have established many fundamental aspects of the specificity and rate of substrate transport in EmrE, low resolution of available structures has hampered identification of the transport coupling mechanism. Here we present a complete, refined atomic structure of EmrE optimized against available cryo-electron microscopy (cryo-EM) data to delineate the critical interactions by which EmrE regulates its conformation during the transport process. With the model, we conduct molecular dynamics simulations of the transporter in explicit membranes to probe EmrE dynamics under different substrate loading and conformational states, representing different intermediates in the transport cycle. The refined model is stable under extended simulation. The water dynamics in simulation indicate that the hydrogen-bonding networks around a pair of solvent-exposed glutamate residues (E14) depend on the loading state of EmrE. One specific hydrogen bond from a tyrosine (Y60) on one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. The hydrogen bond provided by Y60 lowers the pKa of one glutamate relative to the other, suggesting both glutamates should be protonated for the hydrogen bond to break and a substrate-free transition to take place. These findings establish the molecular mechanism for the coupling between proton transfer reactions and protein conformation in this proton-coupled secondary transporter.
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TAYYAB, SAAD, TUAN NOR NAZIAN TUAN MAT, and ADYANI AZIZAH ABD HALIM. "DIFFERENTIAL STABILIZING EFFECTS OF BUFFERS ON STRUCTURAL STABILITY OF BOVINE SERUM ALBUMIN AGAINST UREA DENATURATION." Latin American Applied Research - An international journal 52, no. 1 (January 1, 2022): 7–13. http://dx.doi.org/10.52292/j.laar.2022.738.
Full textAbstract:
The conformational stability of bovine serum albumin (BSA) against urea denaturation was investigated in aqueous solutions both in the absence and presence of buffers. Various buffers differing in polar and nonpolar characters such as sodium phosphate, Tris-HCl, (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) HEPES and [3-(N-morpholino)propanesulfonic acid] MOPS buffers were used in this study. Urea-induced structural changes were analyzed using different probes, i.e., intrinsic fluorescence, ANS fluorescence and UV-difference spectral signal. Presence of different buffers in the incubation medium offered different degrees of resistance to the protein against urea-induced structural changes compared to those obtained in water (in the absence of buffers). A similar trend of buffer-induced structural resistance was noticed with three different probes. The stabilizing effect of these buffers followed the order: MOPS > HEPES > sodium phosphate > Tris-HCl > water. As found in MOPS and HEPES buffers, the highest stability of BSA can be attributed to the presence of morpholine and piperazine rings, respectively, in their structures. These groups might have produced a hydrophobic environment around the protein surface, thus stabilizing protein conformation against urea denaturation.
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Verdoucq, Lionel, Alexandre Grondin, and Christophe Maurel. "Structure–function analysis of plant aquaporin AtPIP2;1 gating by divalent cations and protons." Biochemical Journal 415, no. 3 (October 15, 2008): 409–16. http://dx.doi.org/10.1042/bj20080275.
Full textAbstract:
Water channel proteins, AQPs (aquaporins), of the PIP (plasma membrane intrinsic protein) subfamily, provide a means for fine and quick adjustments of the plant water status. A molecular model for gating of PIPs by cytosolic protons (H+) and divalent cations was derived from the atomic structure of spinach SoPIP2;1 (Spinacia oleracea PIP2;1) in an open- and a closed-pore conformation. In the present study, we produced the Arabidopsis AtPIP2;1 (Arabidopsis thaliana PIP2;1) homologue in Pichia pastoris, either WT (wild-type) or mutations at residues supposedly involved in gating. Stopped-flow spectrophotometric measurements showed that, upon reconstitution in proteoliposomes, all forms function as water channels. The first functional evidence for a direct gating of PIPs by divalent (bivalent) cations was obtained. In particular, cadmium and manganese were identified, in addition to calcium (Ca2+) and H+ as potent inhibitors of WT AtPIP2;1. Our results further show that His199, the previously identified site for H+ sensing, but also N-terminal located Glu31, and to a lesser extent Asp28, are involved in both divalent-cation- and H+-mediated gating. In contrast, mutation of Arg124 rendered AtPIP2;1 largely insensitive to Ca2+ while remaining fully sensitive to H+. The role of these residues in binding divalent cations and/or stabilizing the open or closed pore conformations is discussed.
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Olaposi, Omotuyi I., Nash Oyekanmi, Metibemu D. Samuel, Ojochenemi A. Enejoh, Ukwenya O. Victor, and Adelakun Niyi. "Takeda G-protein Receptor (TGR)-5 Evolves Classical Activestate Conformational Signatures in Complex with Chromolaena Odorata-derived Flavonoid-5,7-dihydroxy-6-4-dimethoxyflavanone." Current Chemical Biology 13, no. 3 (November 14, 2019): 212–22. http://dx.doi.org/10.2174/2212796813666190102102018.
Full textAbstract:
Background: Takeda G-protein receptor 5 (TGR5) via glucagon-like peptide release and insulin signaling underlies antidiabetic roles of TGR5 agonists. Chromolaena Odorata- derived flavonoid-5,7-dihydroxy-6-4-dimethoxyflavanone (COF) has been identified as (TGR5) agonist. The structural basis for their interaction has not been studied. Objective: This study aimed at providing both structural and dynamic insights into COF/TGR5 interaction. Methods: Classical GPCR activation signatures (TMIII-TMVI ionic lock, toggle switches, internal water pathway) using classical MD simulation have been used. Results: Y893.29, N933.33 and E1695.43 are key residues found to be involved in ligand binding; the continuous internal water pathway connects hydrophilic groups of the ligand to the TMIII-TMVI interface in COF-bound state, TMIII-TMVI ionic locks ruptures in COF-TGR5 complex but not antagonist-bound state, and ruptured ionic lock is associated with the evolution of active-state “VPVAM” (analogous to “NPxxY”) conformation. Dihedral angles (c2) calculated along the trajectory strongly suggest W2376.48 as a ligand-dependent toggle switch. Conclusion: TGR5 evolves active state conformation from a starting intermediate state conformation when bound to COF, which further supports its underlying anti-diabetic activities.