Surface plasmon resonance studies of wild-type and AV77 tryptophan repressor resolve ambiguities in super-repressor activity

Functional motifs in Escherichia coli NC101

Escherichia coli (E. coli) bacteria can damage DNA of the gut lining cells and may encourage the development of colon cancer according to recent reports. Genetic switches are specific sequence motifs and many of them are drug targets. It is interesting to know motifs and their location in sequences. At the present study, Gibbs sampler algorithm was used in order to predict and find functional motifs in E. coli NC101 contig 1. The whole genomic sequence of Escherichia coli NC101 contig 1 were retrieved from http://www.ncbi.nlm.nih.gov (NCBI Reference sequence: NZ_AEFA01000001.1) in order to be analyzed with DAMBE software and BLAST. The results showed that the 6-mer motif is CUGGAA in most sequences (genes1-3, 8, 9, 12, 14-18, 20-23, 25, 27, 29, 31-34), CUUGUA for gene 4 , CUGUAA for gene 5, CUGAUG for gene 6, CUGAUA for gene7, CUGAAA for genes 10, 11, 13, 26, 28, and CUGGAG for gene 19, and CUGGUA for gene30 in E. coli NC101 contig 1. It is concluded that the 6-mer motif is CUGGAA in most sequences in E. coli NC101 contig1. The present study may help experimental studies on elucidating the pharmacological and phylogenic functions of the motifs in E. coli.

Backbone amide dynamics studies of Apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the (15)N NMR relaxation profiles of wild-type and A77V mutant Apo-TrpR repressors

Backbone amide dynamics studies were conducted on a temperature-sensitive mutant (L75F-TrpR) of the tryptophan repressor protein (TrpR) of Escherichia coli in its apo (i.e., no l-tryptophan corepressor-bound) form. The (15)N NMR relaxation profiles of apo-L75F-TrpR were analyzed and compared to those of wild-type (WT) and super-repressor mutant (A77V) TrpR proteins, also in their apo forms. The (15)N NMR relaxation data ((15)N-T(1), (15)N-T(2), and heteronuclear (15)N-{(1)H}-nOe) recorded on all three aporepressors at a magnetic field strength of 600 MHz ((1)H Larmor frequency) were analyzed to extract dynamics parameters, including diffusion tensor ratios (D(∥)/D(⊥)), correlation times (τ(m)) for overall reorientations of the proteins in solution, reduced spectral density terms [J(eff)(0), J(0.87ω(H)), J(ω(N))], and generalized order parameters (S(2)), which report on protein internal motions on the picosecond to nanosecond and slower microsecond to millisecond chemical exchange time scales. Our results indicate that all three aporepressors exhibit comparable D(∥)/D(⊥) ratios and characteristic time constants, τ(m), for overall global reorientation, indicating that in solution, all three apoproteins display very similar overall shape, structure, and rotational diffusion properties. Comparison of (15)N NMR relaxation data, reduced spectral density profiles, and generalized S(2) order parameters indicated that these parameters are quite uniform for backbone amides positioned within the four (A-C and F) core α-helices of all three aporepressors. In contrast, small but noticeable differences in internal dynamics were observed for backbone amides located within the helix D-turn-helix E DNA-binding domain of the apo-TrpR proteins. The significance of these dynamics differences in terms of the biophysical characteristics and ligand binding properties of the three apo-TrpR proteins is discussed.

The Tumbleweed: towards a synthetic proteinmotor

Biomolecular motors have inspired the design and construction of artificial nanoscale motors and machines based on nucleic acids, small molecules, and inorganic nanostructures. However, the high degree of sophistication and efficiency of biomolecular motors, as well as their specific biological function, derives from the complexity afforded by protein building blocks. Here, we discuss a novel bottom-up approach to understanding biological motors by considering the construction of synthetic protein motors. Specifically, we present a design for a synthetic protein motor that moves along a linear track, dubbed the "Tumbleweed." This concept uses three discrete ligand-dependent DNA-binding domains to perform cyclically ligand-gated, rectified diffusion along a synthesized DNA molecule. Here we describe how de novo peptide design and molecular biology could be used to produce the Tumbleweed, and we explore the fundamental motor operation of such a design using numerical simulations. The construction of this and more sophisticated protein motors is an exciting challenge that is likely to enhance our understanding of the structure-function relationship in biological motors.

Survey of the year 2003 commercial optical biosensor literature

In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.