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Yi Xia

Publications and source records attributed to Yi Xia.

21 records · Page 2Linked to original sources

Unfolding of rabbit muscle creatine kinase induced by acid. A study using electrospray ionization mass spectrometry, isothermal titration calorimetry, and fluorescence spectroscopy.

Electrospray ionization mass spectrometry, isothermal titration calorimetry (ITC), fluorescence spectroscopy, and glutaraldehyde cross-linking SDS-PAGE have been used to study the unfolding of rabbit muscle creatine kinase (MM-CK) induced by acid. The mass spectrometric experiments show that MM-CK is unfolded gradually when titrated with acid. MM-CK is a dimer (the native state) at pH 7.0 and becomes an equilibrium mixture of the dimer and a partially folded monomer (the intermediate) between pH 6.7 and 5.0. The dimeric protein becomes an equilibrium mixture of the intermediate and an unfolded monomer (the unfolded state) between pH 5.0 and 3.0 and is almost fully unfolded at pH 3.0 reached. The results from a "phase diagram" method of fluorescence show that the conformational transition between the native state and the intermediate of MM-CK occurs in the pH range of 7.0-5.2, and the transition between the intermediate and the unfolded state of the protein occurs between pH 5.2 and 3.0. The intrinsic molar enthalpy changes for formation of the unfolded state of MM-CK induced by acid at 15.0, 25.0, 30.0, and 37.0 degrees C have been determined by ITC. A large positive molar heat capacity change of the unfolding, 8.78 kcal mol-1 K-1, at all temperatures examined indicates that hydrophobic interaction is the dominant driving force stabilizing the native structure of MM-CK. Combining the results from these four methods, we conclude that the acid-induced unfolding of MM-CK follows a "three-state" model and that the intermediate state of the protein is a partially folded monomer.

Acetates↗

Synthesis and bioactivity of 4,10-dimethyl-pyridino[2,3-h]quinolin-2(1H)-one-9-carboxylic acid and its esters.

4,10-Dimethyl-pyridino[2,3-h]quinolin-2(1H)-one-9-carboxylic acid (1) was synthesized by a new approach via the key intermediate 7-[1-aza-2-(dimethylamino)vinyl]-4-methylquinolin-2(1H)-one (4). Compound 1 and its esters were evaluated in cytotoxicity and anti-HIV assays. The 9-carboxyl (1s)-endo-(-)-borneol ester (9) showed marginal cytotoxic activity in CAK1-1, HOS, KB, and HCT-8 cells.

Anti-HIV Agents↗

Accelerating approximate subsequence search on large protein sequence databases.

Bioinformatics has become an active research area in recent years. The amount of mapped sequences doubles every fourteen months. BLAST has been widely employed for retrieving sequences which has similar portion(s) to a given sequence. However, BLAST has to scan the entire database every time when a query is issued. This can be very time consuming especially when the database is large. In this paper, we study the problem on how to build a persistent index structure for protein sequences to support approximate match. The suffix tree has been proposed as a solution to index sequence database and has been deployed on organizing DNA sequences (Hunt et al. 2001). Unfortunately, it suffers from the problem of "memory bottleneck" that prevents it from being applied efficiently to a large database. The performance even degrades further for protein database due to a larger fanout at each node. Here, we employ an indexing structure, called BASS-tree, to support approximate match in sublinear time on a large protein database. We call this indexing method as sequence approximate match (SAM) index method. The search of approximate matches can be properly directed to the portion in the database with a high potential of matching quickly. It has been demonstrated in our experiments that the potential performance improvement is in an order of magnitude over alternative methods such as the BLAST algorithm and the suffix tree.

Algorithms↗