protein-water interface Dotaz Zobrazit nápovědu
To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
- MeSH
- DNA vazebné proteiny chemie MeSH
- DNA chemie MeSH
- fosfáty MeSH
- interpretace statistických dat MeSH
- konformace nukleové kyseliny MeSH
- konformace proteinů MeSH
- molekulární modely MeSH
- vazba proteinů MeSH
- voda chemie MeSH
- výpočetní biologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The effect of non-denaturing concentrations of three different organic solvents, formamide, acetone and isopropanol, on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA at the protein-solvent interface was studied using molecular dynamics simulations. Analysis of B-factors revealed that the presence of a given organic solvent mainly affects the dynamical behavior of the specificity-determining cap domain, with the exception of DbjA in acetone. Orientation of organic solvent molecules on the protein surface during the simulations was clearly dependent on their interaction with hydrophobic or hydrophilic surface patches, and the simulations suggest that the behavior of studied organic solvents in the vicinity of hyrophobic patches on the surface is similar to the air/water interface. DbjA was the only dimeric enzyme among studied haloalkane dehalogenases and provided an opportunity to explore effects of organic solvents on the quaternary structure. Penetration and trapping of organic solvents in the network of interactions between both monomers depends on the physico-chemical properties of the organic solvents. Consequently, both monomers of this enzyme oscillate differently in different organic solvents. With the exception of LinB in acetone, the structures of studied enzymes were stabilized in water-miscible organic solvents.
- MeSH
- 2-propanol chemie farmakologie MeSH
- aceton chemie farmakologie MeSH
- formamidy chemie farmakologie MeSH
- hydrofobní a hydrofilní interakce MeSH
- hydrolasy chemie MeSH
- krystalografie rentgenová MeSH
- kvarterní struktura proteinů účinky léků MeSH
- molekulární modely MeSH
- rozpouštědla chemie MeSH
- simulace molekulární dynamiky MeSH
- terciární struktura proteinů účinky léků MeSH
- voda chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
- MeSH
- krystalografie rentgenová MeSH
- lidé MeSH
- motiv rozpoznávající RNA genetika MeSH
- mutageneze cílená MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- rekombinantní proteiny chemie genetika metabolismus MeSH
- RNA metabolismus MeSH
- sestřihové faktory chemie genetika metabolismus MeSH
- simulace molekulární dynamiky MeSH
- substituce aminokyselin MeSH
- vazebná místa MeSH
- voda chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The surfaces of aqueous solutions are traditionally viewed as devoid of inorganic ions. Molecular simulations and surface-selective spectroscopic techniques show, however, that large polarizable anions and hydronium cations can be found (and even enhanced) at the surface and are involved in chemistry at the air/water interface. Here, we review recent studies of ions at the air/water interface and compare from this perspective water with other polar solvents. For water, we focus in particular on the surface behavior of its ionic product (i.e., hydronium and hydroxide ions). We also investigate the feasibility of dielectric models for the description of the protein/water interface, in analogy to the air/water interface. Little correlation is found between these two interfaces in terms of ion segregation. Therefore, we suggest a local model of pairing of ions from the solution with charged and polar groups at the protein surface. We also describe corresponding results of experimental studies on aqueous model systems.
Photosystem II (PSII) is an intrinsic membrane protein complex that functions as a light-driven water:plastoquinone oxidoreductase in oxygenic photosynthesis. Electron transport in PSII is associated with formation of reactive oxygen species (ROS) responsible for oxidative modifications of PSII proteins. In this study, oxidative modifications of the D1 and D2 proteins by the superoxide anion (O2•-) and the hydroxyl (HO•) radicals were studied in WT and a tocopherol cyclase (vte1) mutant, which is deficient in the lipid-soluble antioxidant α-tocopherol. In the absence of this antioxidant, high-resolution tandem mass spectrometry was used to identify oxidation of D1:130E to hydroxyglutamic acid by O2•- at the PheoD1 site. Additionally, D1:246Y was modified to either tyrosine hydroperoxide or dihydroxyphenylalanine by O2•- and HO•, respectively, in the vicinity of the nonheme iron. We propose that α-tocopherol is localized near PheoD1 and the nonheme iron, with its chromanol head exposed to the lipid-water interface. This helps to prevent oxidative modification of the amino acid's hydrogen that is bonded to PheoD1 and the nonheme iron (via bicarbonate), and thus protects electron transport in PSII from ROS damage.
- MeSH
- alfa-tokoferol chemie metabolismus MeSH
- aminokyseliny chemie metabolismus MeSH
- Arabidopsis enzymologie genetika účinky záření MeSH
- fotosyntéza fyziologie účinky záření MeSH
- fotosystém II - proteinový komplex chemie genetika metabolismus MeSH
- hydroxylový radikál chemie metabolismus MeSH
- interakční proteinové domény a motivy MeSH
- intramolekulární transferasy chemie genetika metabolismus MeSH
- konformace proteinů, alfa-helix MeSH
- konformace proteinů, beta-řetězec MeSH
- kyslík chemie metabolismus MeSH
- molekulární modely MeSH
- mutace MeSH
- oxidace-redukce MeSH
- superoxidy chemie metabolismus MeSH
- světlo MeSH
- termodynamika MeSH
- Thermosynechococcus enzymologie genetika účinky záření MeSH
- tylakoidy enzymologie genetika účinky záření MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- železo chemie metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Nanobubbles formed on monocrystalline gold/water interface by means of the ethanol-to-water solvent exchange were exposed to the solutions of either bovine serum albumin or papain proteins. Both proteins do not change the position of nanobubbles in water, as observed by in situ tapping mode atomic force microscopy imaging before and after the introduction of the protein. The aqueous environment was subsequently replaced by ethanol. While all nanobubbles were found to dissolve in ethanol in the presence of bovine serum albumin, most of them survived when papain was employed. The protective ability of papain was ascribed to its resistance towards the protein denaturation in aqueous solutions of ethanol. The authors employed in situ atomic force nanolithography to investigate the nanomorphology of the papain/nanobubble assemblies in ethanol.
- MeSH
- ethanol chemie MeSH
- nanostruktury chemie MeSH
- papain metabolismus MeSH
- povrchové vlastnosti MeSH
- sérový albumin hovězí metabolismus MeSH
- skot MeSH
- voda chemie MeSH
- zlato metabolismus MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cholesteryl hemisuccinate (CHS) is one of the cholesterol-mimicking detergents not observed in nature. It is, however, widely used in protein crystallography, in biochemical studies of proteins, and in pharmacology. Here, we performed an extensive experimental and theoretical study on the behavior of CHS in lipid membranes rich in unsaturated phospholipids. We found that the deprotonated form of CHS (that is the predominant form under physiological conditions) does not mimic cholesterol very well. The protonated form of CHS does better in this regard, but also its ability to mimic the physical effects of cholesterol on lipid membranes is limited. Overall, although ordering and condensing effects characteristic to cholesterol are present in systems containing any form of CHS, their strength is appreciably weaker compared to cholesterol. Based on the considerable amount of experimental and atomistic simulation data, we conclude that these differences originate from the fact that the ester group of CHS does not anchor it in an optimal position at the water-membrane interface. The implications of these findings for considerations of protein-cholesterol interactions are briefly discussed.
- MeSH
- 2-naftylamin analogy a deriváty chemie MeSH
- cholesterol chemie MeSH
- dihydropyridiny chemie MeSH
- estery cholesterolu chemie MeSH
- fosfatidylcholiny chemie MeSH
- laurany chemie MeSH
- lipidové dvojvrstvy chemie MeSH
- liposomy chemie MeSH
- protony * MeSH
- simulace molekulární dynamiky MeSH
- voda chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.
The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein-DNA crystal structures were analyzed [Schneider et al. (2014), Nucleic Acids Res. 42, 3381-3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein-protein or protein-DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.
- MeSH
- DNA chemie MeSH
- krystalografie rentgenová metody MeSH
- proteiny chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
