An alcohol and anesthetic binding pocket is hypothesized to exist among transmembrane domains of the α1 glycine receptor (GlyR). Prior work has shown that amino acid residue serine-267 plays a significant role in the enhancing effects of alcohol and anesthetics and is theorized to form part of an alcohol and anesthetic binding cavity among subunit transmembrane domains. Propyl methanethiosulfonate (PMTS), an alcohol-like thiol, was previously shown to bind to a cysteine residue introduced at position 267 (S267C) and this resulted in permanent enhancement of GlyR function. If ethanol is binding to residue 267 in wildtype GlyR to potentiate receptor function then we hypothesized that covalent thiol labeling would produce receptor enhancement by the same mechanisms as ethanol. Using outside-out patch single channel electrophysiology we determined the open and closed dwell-times and burst properties of S267C GlyR in the absence and presence of PMTS. The primary consequence of PMTS binding to S267C GlyR was an increase in the lengths of burst durations, paralleling the main effect of ethanol on wildtype GlyR. Our findings thus provide a new line of evidence suggesting that ethanol is exerting its enhancing effects on the GlyR through its interactions with amino acid residue 267 in the second transmembrane domain. / text

The work undertaken within this thesis is towards the development of a representative set of sequence driven features for the prediction of structural classes of proteins. Proteins are biological molecules that make living things function, to determine the function of a protein the structure must be known because the structure dictates its physical capabilities. A protein is generally classified into one of the four main structural classes, namely all-α, all-β, α + β or α / β, which are based on the arrangements and gross content of the secondary structure elements. Current methods manually assign the structural classes to the protein by manual inspection, which is a slow process. In order to address the problem, this thesis is concerned with the development of automated prediction of structural classes of proteins and extraction of a small but robust set of sequence driven features by using the amino acid indices. The first main study undertook a comprehensive analysis of the largest collection of sequence driven features, which includes an existing set of 1479 descriptor values grouped by ten different feature groups. The results show that composition based feature groups are the most representative towards the four main structural classes, achieving a predictive accuracy of 63.87%. This finding led to the second main study, development of the generalised amino acid composition method (GAAC), where amino acid index values are used to weigh corresponding amino acids. GAAC method results in a higher accuracy of 68.02%. The third study was to refine the amino acid indices database, which resulted in the highest accuracy of 75.52%. The main contributions from this thesis are the development of four computationally extracted sequence driven feature-sets based on the underused amino acid indices. Two of these methods, GAAC and the hybrid method have shown improvement over the usage of traditional sequence driven features in the context of smaller and refined feature sizes and classification accuracy. The development of six non-redundant novel sets of the amino acid indices dataset, of which each are more representative than the original database. Finally, the construction of two large 25% and 40% homology datasets consisting over 5000 and 7000 protein samples, respectively. A public webserver has been developed located at http://www.generalised-protein-sequence-features.com, which allows biologists and bioinformaticians to extract GAAC sequence driven features from any inputted protein sequence.

Sun Qiang. / "December 1999." / Thesis (Ph.D.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (p. 119-139). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

Wong Ka Shing = 兩個二級蛋白質結構組中的氨基酸序列的統計特性 / 黃嘉誠. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 88-91). / Text in English; abstracts in English and Chinese. / Wong Ka Shing = Liang ge er ji dan bai zhi jie gou zu zhong de an ji suan xu lie de tong ji te xing / Huang Jiacheng. / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Predicting tertiary structures of proteins --- p.2 / Chapter 1.2 --- Introduction to secondary structures of protein --- p.5 / Chapter 1.3 --- Prediction of secondary structural classes --- p.9 / Chapter 1.3.1 --- Multi-dimensional space representation --- p.10 / Chapter 2 --- Method of analysis --- p.12 / Chapter 2.1 --- Data sets --- p.12 / Chapter 2.2 --- Basic statistics of the data sets --- p.13 / Chapter 2.3 --- Method of analysis --- p.17 / Chapter 2.4 --- An interesting sum rule --- p.20 / Chapter 3 --- Results of analysis of C-words --- p.22 / Chapter 3.1 --- A first insight --- p.22 / Chapter 3.2 --- Distributions of 〈C(j)〉 --- p.24 / Chapter 3.2.1 --- "Comparing distributions for different m, s and secondary structural classes" --- p.29 / Chapter 3.3 --- Features of each secondary structural class --- p.33 / Chapter 3.3.1 --- C-words with the largest or the smallest values of 〈C(j)〉 in the all-a class --- p.33 / Chapter 3.3.2 --- C-words with the largest or the smallest values of 〈C(j)〉 in the all-β class --- p.35 / Chapter 4 --- Results of analysis of H-words --- p.37 / Chapter 4.1 --- 〈C(j)〉 for each H-word --- p.38 / Chapter 4.1.1 --- "When m increases, 〈C(j)〉 deviates more from 1" --- p.39 / Chapter 4.1.2 --- "When spacing parameter s is small, 〈C(j)〉 deviates more from 1" --- p.40 / Chapter 4.2 --- The mean over all possible H-words --- p.41 / Chapter 4.3 --- Comparing 〈C(j)〉 of different H-words --- p.43 / Chapter 4.3.1 --- A few plots --- p.43 / Chapter 4.3.2 --- Results --- p.44 / Chapter 4.4 --- Features of each secondary structural class --- p.47 / Chapter 4.4.1 --- A first insight --- p.47 / Chapter 4.4.2 --- The H-words with the largest values of 〈C(j)〉 in the all-α class with particular number of letter m --- p.54 / Chapter 4.4.3 --- The H-words with the smallest values of 〈C(j) in the all-α class with particular number of letter m --- p.57 / Chapter 4.4.4 --- The H-words with the largest values of 〈C(j) in the all-β class with particular number of letter m --- p.60 / Chapter 4.4.5 --- The H-words with the smallest values of 〈C(j) in the all-β class with particular number of letter m --- p.63 / Chapter 4.4.6 --- A summary --- p.66 / Chapter 4.5 --- Possible indicators to predict secondary structural class --- p.67 / Chapter 4.5.1 --- H-words with the largest values of --- p.68 / Chapter 4.5.2 --- H-words with the largest magnitude of --- p.71 / Chapter 4.5.3 --- Discussion --- p.71 / Chapter 5 --- Prediction using patterns found in H-words --- p.72 / Chapter 6 --- Conclusion --- p.86 / Bibliography --- p.88

With the aim to enhance the efficiency of utilization of crystalline methionine supplemented in the high plant-protein diet for grouper (Epinephelus coioides), this study used Bacillus subtitlis spore as a probiotic additive in the diet to shorten the absorption time difference between protein-bound amino acid and crystalline methionine. The study was conducted in two parts. In the first part, juvenile groupers were fed for 14 weeks with 5 experimental diets: fish meal diet, high plant-protein diet with/without crystalline methionine, as well as with/without B. subtitlis spore separately. Growth performance, PER, protein digestibility, amino acid digestibility, non-specific immune responses, and free amino acid concentration in both muscle and serum were assessed. The second part was a time-series study on serum free amino acids concentration after a force-feeding experiment. The results showed that crystalline methionine supplementation in the high plant-protein diet effectively improved the growth of E. coioides (P<0.05). However, B. subtitlis spore supplementation did not affect fish growth performance significantly (P>0.05). A delay in the appearance of peak serum amino acid concentration was observed when fishmeal was partially replaced by soy protein. On the other hand, the force-feeding experiment showed that serum essential amino acid (include methionine) concentrations droped drastically after they reached the peak concentrations from being forced-fed with the B. subtilis containing diet. Supplementation of crystalline methionine seemed to ease the drop of serum methionine concentration. Based on these results, it is concluded that addition of B. subtitlis spore in high plant-protein diet for the grouper does not enhance the utilization of crystalline methionine, but supplementation of crystalline methionine significantly improve the growth performance of the grouper.

Diss. (sammanfattning) Stockholm : Karol. inst., 2002. / Härtill 6 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 5 uppsatser.

Thesis (doctoral)--Lund University, 1997. / Added t.p. with thesis statement inserted.

Thesis (doctoral)--Lund University, 1997. / Added t.p. with thesis statement inserted.

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 210 pages. Includes Vita. Includes bibliographical references.