Search

The study explains the role and effects of various aromatic side chains in the photoactivation of BLUF (blue-light sensing using FAD) domain proteins. The analysis proves the presence of two competing light-driven electron-transfer pathways in BLUF domains that make them effective blue-light sensing receptors.

Research has been conducted on the carbohydrate-binding peptides. The reactivity of these peptides has been investigated and the results are presented.

The interaction between nisin and lipid II in a membrane environment, provided by sodium dodesylsulfate micelles, is studied by solution nuclear magnetic resonance spectroscopy. Research shows that only the N-terminal part of nisin interacts with lipid II with C-terminus unaffected. Nisin mediated membrane pore forming mechanism is a multistep process.

Research has been conducted on the photoactive yellow protein from Ectothiorhodospira halophila. The probing of the pB intermediate's nature of this protein by NMR spectroscopy is described and the results are presented.

Differences in dynamics seen in retinoid X receptor (RXR) free in solution and in complex with a 14-base-pair DNA half-site have been investigated. Lipari-Szabo analysis was used with an axially symmetric tumbling model to gather information about the exchange contribution to the transverse relaxation rates. When DNA-binding had taken place the order parameters were slightly greater. Dynamics in the millisecond to microsecond range were seen more. The DNA-binding-induced folding transition takes place far from the DNA in an area involved in protein-protein interaction. Thus it may be that it is related to the cooperation of dimeric DNA-binding.

Research was conducted to examine the solution structure of the hyperstable MYL mutant of the Arc repressor of bacteriophage P22 using NMR spectroscopy and to compare it to that of the wild-type Arc repressor. It was observed that the premelting transition mainly entails a conformational change at Phe 10 and repacking of the hydrophobic core. The structural investigation demonstrate a dynamic character of the beta-sheet region in the Arc repressor which is supported by 15N relaxation and hydrogen-deuterium exchange data.

The 9-cis retinoic acid receptor (RXR) and the all-trans retinoic acid receptor (RAR) are members of a family of ligand inducible transcription factors. Nuclear receptors belonging to the Class II sub-family, RXR and RAR both bind to DNA as dimers, on tandem repeats of a hexamer motif separated by a variable spacer. The DNA-binding domains of RXR and RAR have zinc-coordinating loop regions that exhibit millisecond to microsecond time scale dynamics. A functional role for the dynamics is suggested by the close association between regions of conformational exchange and dimer interfaces.

A study was conducted to characterize the structure of a photosensory protein from Ectothiorhodopsin halophila called photoactive yellow protein. Multidimensional nuclear magnetic resonance spectroscopy was carried out to determine selected structures and a root-mean-square deviation. Results indicated differences in the crystal structure located in the n-terminus which established lariat-like loop structure.

A research was conducted to investigate transportability of glycans as part of intact glycoproteins. Nuclear magnetic resonance (NMR) spectra was measured between 328 and 338K on a Bruker AMX 500 instrument while NMR data sets were determined using the Bruker UXNMR software. Results indicated that the protein part of the alpha-subunit of human chorionic gonadotropin influenced the dynamic behavior of the glycan at Asn79. Moreover, the inner core mobility of the glycan was significantly limited by protein attachments.

The three-dimensional solution structure of the immunodominant central conserved region of the attachment protein G (BRSV-G) of bovine respiratory syncytial virus was determined by nuclear magnetic resonance spectroscopy. In the 32-residue peptide examined, 19 residues form a small rigid core composed of two short helices, connected by a type I' turn, and linked by two disulfide bridges.

The structure of the E. coli LexA repressor complex was studied by affinity cleavage and affinity photo-cross-linking. Cysteine residues were introduced in 7, 28, 38, or 52 positions of the protein with arginine as the original amino acid. The cysteine side chains were incorporated with EDTA-iron or phenyl azide. Alkali/heat treatment determined cross-linking in the phenyl azide derivatives while EDTA-iron derivatives cleaved with DNA near the amino acid.

The helix of the signal peptide of PhoE of Escherichia coli is present from Lys3 of the N-terminal to Ser18 in a homogenous membrane such as trifluoroethanol while in anionic membranes such as sodium dodecyl sulfate micelles the helix is present from Lys2 to Ser 18. In zwitterionic lipids such as dodecylphosphocholine micelles the helix goes not extend very far in the N-terminal and the C-terminal structure is not very flexible. In all cases the helix is weak at Gly12 position. These conformational changes in the signal peptide of proteins are required for the export of the proteins.

NMR studies of the solution structure of dimeric Mnt repressor (1-76) shows the presence of functionally distinct N and C-terminal regions. The N-terminus of Mnt is sequentially similar to that of the Arc repressor, having an analogous secondary and tertiary structure. This region mediates DNA binding and dimer formation. The C-terminus of Mnt has an unstable third helix and is crucial for tetramer formation.

Double and triple-resonance 2D and 3D NMR experiments enable assignment of most of the observable protons in 1H, 13C and 5N for the HU protein from Bacillus stearothermophilus and conformation of the antiparallel beta-hairpin in the DNA-binding region of the HU protein. Chemical shifts of different nuclei, proton exchange data and NOEs help analyze the secondary structures. X-ray analysis confirms the arrangement of three extended strands and three alpha-helices proposed by these studies.

Two-dimensional homo-and heteronuclear nuclear magnetic resonance (NMR) methods, three-dimensional heteronuclear NMR methods, TOCSY, 2D NOE, and NOESY-HMQC experiments were used in the orderly assignment of the H and N resonances of the POU-specific DNA-binding domain of transcription factor Oct-1.

Porcine pancreatic phospholipase A2 (PLA) was studied with respect to 1H and 15N chemical shifts, amide exchange rates and nuclear Overhauser effect intensities for the enzyme in solution, in a binary complex with dodecylphosphocholine micelles and in a ternary complex with a micelle and the substrate-like inhibitor. Structural differences associated with the three environments and with the presence of the competitive inhibitor were observed. On the basis of analysis of nuclear magnetic resonance data, a two-step mechanism for PLA activation is proposed.

The structure of the tandem zinc-finger region of human ZHX1 protein related to the occurrence of certain cancers was determined to understand the function and structure of the individual ZHX domains. The results showed that both zinc-fingers (ZNF1 and ZNF2) adopted canonical [beta][beta][alpha]-folds in which a zinc ion is coordinated by two cysteine and two histidine residues while the C-terminal extension to ZNF2 forms two [beta]-strands to form a [beta]-sheet with the [beta]-strands of this zinc-finger.