Search results for "protein conformation"
showing 10 items of 515 documents
The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV-vis absorption spectroscopy study.
2021
AbstractSolvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation…
The non-bilayer lipid MGDG stabilizes the major light-harvesting complex (LHCII) against unfolding.
2017
Abstract In the photosynthetic apparatus of plants a high proportion of LHCII protein is needed to integrate 50% non-bilayer lipid MGDG into the lamellar thylakoid membrane, but whether and how the stability of the protein is also affected is not known. Here we use single-molecule force spectroscopy to map the stability of LHCII against mechanical unfolding along the polypeptide chain as a function of oligomerization state and lipid composition. Comparing unfolding forces between monomeric and trimeric LHCII demonstrates that the stability does not increase significantly upon trimerization but can mainly be correlated with specific contact sites between adjacent monomers. In contrast, unfol…
A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid
2008
Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use mo…
NMR Solution Structure of the Non-RGD Disintegrin Obtustatin
2003
The solution structure of obtustatin, a novel non-RGD disintegrin of 41 residues isolated from Vipera lebetina obtusa venom, and a potent and selective inhibitor of the adhesion of integrin alpha(1)beta(1) to collagen IV, has been determined by two-dimensional nuclear magnetic resonance. Almost the whole set of chemical shifts for 1H, 13C and 15N were assigned at natural abundance from 2D homonuclear and heteronuclear 500 MHz, 600 MHz and 800 MHz spectra at pH 3.0 recorded at 298 K and 303 K. Final structural constraints consisted of 302 non-redundant NOE (95 long-range, 60 medium, 91 sequential and 56 intra-residue), four disulfide bond distances, five chi1 dihedral angles and four hydroge…
Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class o…
2000
AbstractBackground: Epoxide hydrolases have important roles in the defense of cells against potentially harmful epoxides. Conversion of epoxides into less toxic and more easily excreted diols is a universally successful strategy. A number of microorganisms employ the same chemistry to process epoxides for use as carbon sources.Results: The X-ray structure of the epoxide hydrolase from Aspergillus niger was determined at 3.5 Å resolution using the multiwavelength anomalous dispersion (MAD) method, and then refined at 1.8 Å resolution. There is a dimer consisting of two 44 kDa subunits in the asymmetric unit. Each subunit consists of an α/β hydrolase fold, and a primarily helical lid over the…
Jararhagin-derived RKKH Peptides Induce Structural Changes in α1I Domain of Human Integrin α1β1
2003
Integrin alpha(1)beta(1) is one of four collagen-binding integrins in humans. Collagens bind to the alphaI domain and in the case of alpha(2)I collagen binding is competitively inhibited by peptides containing the RKKH sequence and derived from the metalloproteinase jararhagin of snake venom from Bothrops jararaca. In alpha(2)I, these peptides bind near the metal ion-dependent adhesion site (MIDAS), where a collagen (I)-like peptide is known to bind; magnesium is required for binding. Published structures of the ligand-bound "open" conformation of alpha(2)I differs significantly from the "closed" conformation seen in the structure of apo-alpha(2)I near MIDAS. Here we show that two peptides,…
Conformational investigation of alpha,beta-dehydropeptides. XIII. Conformational properties of N-acetyl-alpha,beta-dehydrovaline N',N'-dimethylamide.
2004
The crystal structure of Ac-DeltaVal-NMe(2) (DeltaVal = alpha,beta-dehydrovaline) was determined by X-ray crystallography. The found angles phi = -60 degrees and psi = 125 degrees correspond exactly to the respective values of the (i + 1)th residue in idealised beta-turn II/VIa. Ab initio/DFT studies revealed that the molecule adopts the angle psi restricted only to about |130 degrees | and very readily attains the angle phi = about -50 degrees. This is in line with its solid-state conformation. Taken together, these data suggest that the DeltaVal residue combined with a C-terminal tertiary amide is a good candidate at the (i + 1)th position in a type II/VIa beta-turn.
Activation of Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus by Removal of Magnesium Inhibition and Acceleration of Product Rele…
2009
Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Sulfolobus solfataricus (ssAnPRT) is encoded by the sstrpD gene and catalyzes the reaction of anthranilate (AA) with a complex of Mg(2+) and 5'-phosphoribosyl-alpha1-pyrophosphate (Mg.PRPP) to N-(5'-phosphoribosyl)-anthranilate (PRA) and pyrophosphate (PP(i)) within tryptophan biosynthesis. The ssAnPRT enzyme is highly thermostable (half-life at 85 degrees C = 35 min) but only marginally active at ambient temperatures (turnover number at 37 degrees C = 0.33 s(-1)). To understand the reason for the poor catalytic proficiency of ssAnPRT, we have isolated from an sstrpD library the activated ssAnPRT-D83G + F149S double …
Interfacial behavior of recombinant forms of human pulmonary surfactant protein SP-C.
2012
The behavior at air-liquid interfaces of two recombinant versions of human surfactant protein SP-C has been characterized in comparison with that of native palmitoylated SP-C purified from porcine lungs. Both native and recombinant proteins promoted interfacial adsorption of dipalmitoylphosphatidylcholine bilayers to a limited extent, but catalyzed very rapid formation of films from different lipid mixtures containing both zwitterionic and anionic phospholipids. Once at the interface, the recombinant variants exhibited compression-driven structural transitions, consistent with changes in the orientation of the deacylated N-terminal segment, which were not observed in the native protein. Com…
Tyrosinase/catecholoxidase activity of hemocyanins: structural basis and molecular mechanism
2000
The enzymes tyrosinase, catecholoxidase and hemocyanin all share similar active sites, although their physiological functions differ. Hemocyanins serve as oxygen carrier proteins, and tyrosinases and catecholoxidases (commonly referred to as phenoloxidases in arthropods) catalyze the hydroxylation of monophenols or the oxidation of o-diphenols to o-quinones, or both. Tyrosinases are activated in vivo by limited proteolytic cleavage, which might open up substrate access to the catalytic site. It has recently been demonstrated that if hemocyanins are subjected to similar proteolytic treatments (in vitro) they also exhibit at least catecholoxidase reactivity. On the basis of their molecular st…