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2P-362 Study on the Conformational Distance of Transmembrane Proteins Using Joint-based Descriptor
( Jayaraman Thangappan ),이선구 한국공업화학회 2017 한국공업화학회 연구논문 초록집 Vol.2017 No.1
Joint-based descriptor is a new level of macroscopic descriptor for protein structure using joints of secondary structures as a basic element. Here, we propose how the joint-based descriptor can be applied to examine the conformational distances or differences of transmembrane (TM) proteins. First, the conformational distances of GPCR A family and other 7 TM proteins were evaluated. This provided the information on the distant and close families or superfamilies to GPCR A family and permitted the identification of conserved local conformations. Second, computational models of GPCR A family proteins were validated, which enabled us to estimate how much they reproduce the native conformation of GPCR A proteins at global and local conformational level. Finally, the conformational distances between active and inactive states of GPCR proteins were estimated, which identified the difference of local conformation.
김묘정,조병철,윤현정,우상욱,Jayaraman Thangappan,은창선 한국물리학회 2018 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.72 No.9
The selectivity and conduction specificity of the KcsA channel toward potassium ions is crucial to the activity of this protein and this channel is intricately associated with several osmotic regu- lation and neuronal signaling processes. Despite multi-ion characteristics, the selective conduction behavior of KcsA is controlled by the size and distance specific electrostatic interaction between the selected residues and the potassium ions. The mechanism describing the movement of potassium ions in the channel and the conformational changes to KcsA that facilitate ion movement were investigated by a molecular dynamics (MD) simulation. In this study, we analyze the movement of potassium ions and water molecules at various time intervals during a 90 ns molecular dynamics simulation in the high potassium ion concentration regime and in the absence of the voltage. Examination of specific (3.6, 17.3, 43.38 and 43.44 ns) simulation periods revealed that key residues in the selectivity filter of KcsA in uence the movement of potassium ions in the channel.
Engineering a beta-turn in green fluorescent protein to a foreign loop
Bharat Madan,이선구,Jayaraman Thangappan 한국공업화학회 2016 Journal of Industrial and Engineering Chemistry Vol.33 No.-
A type I beta-turn in green fluorescent protein (GFP) was engineered to a foreign loop. Moleculardynamics simulation study showed that the addition of foreign loop into GFP did not have a negativeinfluence on the conformation stability of GFP structure, but the GFP variant with the foreign loopsequence was completely misfolded in real folding conditions. The co-incorporation of the enhancingmutations for GFP folding made it possible to generate a foldable and active GFP variant with the foreignloop sequence, although the folding efficiency and specific activity of the GFP were negatively affected bythe introduced loop.
Modulation of protein folding rate of GFP through beta-turn engineering
( Bharat Madan ),( Govindan Raghunathan ),( Sriram Sokalingam ),( Thangappan Jayaraman ),( Sungwan Park ),이선구 한국공업화학회 2015 한국공업화학회 연구논문 초록집 Vol.2015 No.1
Control of the protein folding rate is very important in various biological studies and biotechnology. The present study examined the possibility of modulating the protein folding rate through beta-turn engineering of green fluorescence protein (GFP). A type II’ two residue beta-turn in GFP was targeted to generate various sets of mutants. The design of mutants was based on the rationale that residues i+1 and i+2 of a beta-turn have defined residue preferences, and their perturbation affects the rate of protein folding. The in vitro refolding kinetics performed with purified variants showed the variantion of GFP folding rate as expected. This kind of study would be useful in the modulation of in vivo activities of recombinant proteins which have been generally controlled at transcription and translation levels.
Characterization of 1,3-Propanediol Oxidoreductase (DhaT) from Klebsiella pneumoniae J2B
Suman Lama,노수문,설은희,Balaji Sundara Sekar,Satish Kumar Ainala,Jayaraman Thangappan,송효학,승두영,박성훈 한국생물공학회 2015 Biotechnology and Bioprocess Engineering Vol.20 No.6
1,3-propanediol oxidoreductase (DhaT) of Klebsiella pneumoniae converts 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol (1,3-PD) during microbial production of 1,3-PD from glycerol. In this study, DhaT from newly isolated K. pneumoniae J2B was cloned, expressed, purified, and studied for its kinetic properties. It showed, on its physiological substrate 3-HPA, higher activity than similar aldehydes such as acetaldehyde, propionaldehyde and butyraldehyde. The turnover numbers (kcat, 1/s) were estimated as 59.4 for the forward reaction (3-HPA to 1,3-PD at pH 7.0) and 10.0 for the reverse reaction (1,3-PD to 3-HPA at pH 9.0). The Michaelis constants (Km, mM) were 0.77 (for 3-HPA) and 0.03 (for NADH) for the forward reaction (at pH 7.0), and 7.44 (for 1,3-PD) and 0.23 (for NAD+) for the reverse reaction (at pH 9.0). Between these forward and reverse reactions, the optimum temperature and pH were significantly different (37°C and 7.0 vs. 55°C and 9.0, respectively). These results indicate that, under physiological conditions, DhaT mostly catalyzes the forward reaction. The enzyme was seriously inhibited by heavy metal ions such as Ag+ and Hg2+. DhaT was highly unstable when incubated with its own substrate 3-HPA, indicating the necessity of enhancing its stability for improved 1,3-PD production from glycerol.