Latsavongsakda Sethaphong

North Carolina State University, Raleigh, North Carolina, United States

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Publications (10)40.48 Total impact

  • Ho Shin Kim, Sung Ho Ha, Latsavongsakda Sethaphong, Yoon-Mo Koo, Yaroslava G Yingling
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    ABSTRACT: Candida antarctica lipase B (CALB) is an efficient biocatalyst for hydrolysis, esterification, and polymerization reactions. In order to understand how to control enzyme activity and stability we performed a combined experimental and molecular dynamics simulation study of CALB in organic solvents and ionic liquids (ILs). Our results demonstrate that the conformational changes of the active site cavity are directly related to enzyme activity and decrease in the following order: [Bmim][TfO] > tert-butanol > [Bmim][Cl]. The entrance to the cavity is modulated by two isoleucines, ILE-189 and ILE-285, one of which is located on the α-10 helix. The α-10 helix can substantially change its conformation due to specific interactions with solvent molecules. This change is acutely evident in [Bmim][Cl] where interactions of LYS-290 with chlorine anions caused a conformational switch between α-helix and turn. Disruption of the α-10 helix structure results in a narrow cavity entrance and, thus, reduced the activity of CALB in [Bmim][Cl]. Finally, our results show that the electrostatic energy between solvents in this study and CALB is correlated with the structural changes leading to differences in enzyme activity.
    Physical Chemistry Chemical Physics 01/2014; · 3.83 Impact Factor
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    ABSTRACT: A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose-synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs.
    Proceedings of the National Academy of Sciences 04/2013; · 9.81 Impact Factor
  • H. Yi, S. Thakur, L. Sethaphong, Y. G. Yingling
    SPIE Visualization and Data Analysis; 01/2013
  • Abhishek Singh, Latsavongsakda Sethaphong, Yaroslava G. Yingling
    Biophysical Journal 01/2012; 102(3):250-. · 3.67 Impact Factor
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    Abhishek Singh, Latsavongsakda Sethaphong, Yaroslava G Yingling
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    ABSTRACT: RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.
    Biophysical Journal 08/2011; 101(3):727-35. · 3.67 Impact Factor
  • Latsavongsakda Sethaphong, Yaroslava Yingling
    Biophysical Journal 02/2011; 100(3):77-. · 3.67 Impact Factor
  • Andrés Vargas, Latsavongsakda Sethaphong, Yaroslava Yingling
    Biophysical Journal 01/2011; 100(3). · 3.67 Impact Factor
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    ABSTRACT: Sequence dependency of metal ion aggregation around RNA structures is known to be involved in critical functions ranging from processes of molecular recognition to enzymatic chemistry. Ion interactions with an HIV-1 TAR RNA core helix were examined with explicit solvent molecular dynamics simulations. The results have shown that there is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine-rich duplexes. The behavior is independent of ionic species or a presence of a bulge. A region of high ion affinity agrees very well with the position of the X-ray determined divalent cations within a fragment from the HIV-1 TAR RNA.
    The Journal of Physical Chemistry C 01/2010; 114(12):5506. · 4.84 Impact Factor
  • Abhishek Singh, Latsavongsakda Sethaphong, Yaroslava G. Yingling
    Biophysical Journal 01/2010; 98(3). · 3.67 Impact Factor
  • Biophysical Journal 01/2010; 98. · 3.67 Impact Factor