@article{sethaphong_davis_slabaugh_singh_haigler_yingling_2016, title={Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis}, volume={23}, ISSN={0969-0239 1572-882X}, url={http://dx.doi.org/10.1007/s10570-015-0789-6}, DOI={10.1007/s10570-015-0789-6}, number={1}, journal={Cellulose}, publisher={Springer Science and Business Media LLC}, author={Sethaphong, Latsavongsakda and Davis, Jonathan K. and Slabaugh, Erin and Singh, Abhishek and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2016}, month={Feb}, pages={145–161} }
 @article{slabaugh_sethaphong_xiao_amick_anderson_haigler_yingling_2014, title={Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase}, volume={65}, ISSN={1460-2431 0022-0957}, url={http://dx.doi.org/10.1093/jxb/eru383}, DOI={10.1093/jxb/eru383}, abstractNote={The β-1,4-glucan chains comprising cellulose are synthesized by cellulose synthases in the plasma membranes of diverse organisms including bacteria and plants. Understanding structure-function relationships in the plant enzymes involved in cellulose synthesis (CESAs) is important because cellulose is the most abundant component in the plant cell wall, a key renewable biomaterial. Here, we explored the structure and function of the region encompassing transmembrane helices (TMHs) 5 and 6 in CESA using computational and genetic tools. Ab initio computational structure prediction revealed novel bi-modal structural conformations of the region between TMH5 and 6 that may affect CESA function. Here we present our computational findings on this region in three CESAs of Arabidopsis thaliana (AtCESA1, 3, and 6), the Atcesa3(ixr1-2) mutant, and a novel missense mutation in AtCESA1. A newly engineered point mutation in AtCESA1 (Atcesa1(F954L) ) that altered the structural conformation in silico resulted in a protein that was not fully functional in the temperature-sensitive Atcesa1(rsw1-1) mutant at the restrictive temperature. The combination of computational and genetic results provides evidence that the ability of the TMH5-6 region to adopt specific structural conformations is important for CESA function.}, number={22}, journal={Journal of Experimental Botany}, publisher={Oxford University Press (OUP)}, author={Slabaugh, Erin and Sethaphong, Latsavongsakda and Xiao, Chaowen and Amick, Joshua and Anderson, Charles T. and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2014}, month={Sep}, pages={6645–6653} }
 @article{kim_ha_sethaphong_koo_yingling_2014, title={The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study}, volume={16}, ISSN={["1463-9084"]}, url={https://publons.com/publon/389513/}, DOI={10.1039/c3cp52516c}, abstractNote={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.}, number={7}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, publisher={Royal Society of Chemistry (RSC)}, author={Kim, Ho Shin and Ha, Sung Ho and Sethaphong, Latsavongsakda and Koo, Yoon-Mo and Yingling, Yaroslava G.}, year={2014}, pages={2944–2953} }
 @article{sethaphong_haigler_kubicki_zimmer_bonetta_debolt_yingling_2013, title={Tertiary model of a plant cellulose synthase}, volume={110}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1301027110}, DOI={10.1073/pnas.1301027110}, abstractNote={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.}, number={18}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Sethaphong, L. and Haigler, C. H. and Kubicki, J. D. and Zimmer, J. and Bonetta, D. and DeBolt, S. and Yingling, Y. G.}, year={2013}, month={Apr}, pages={7512–7517} }
 @inproceedings{yi_thakur_sethaphong_yingling_2013, title={X3DBio2: A visual analysis tool for biomolecular structure comparison}, volume={8654}, ISSN={["1996-756X"]}, url={http://dx.doi.org/10.1117/12.2002626}, DOI={10.1117/12.2002626}, abstractNote={A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers.
The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.}, booktitle={Visualization and Data Analysis 2013}, publisher={SPIE}, author={Yi, Hong and Thakur, Sidharth and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, editor={Wong, Pak Chung and Kao, David L. and Hao, Ming C. and Chen, Chaomei and Healey, Christopher G.Editors}, year={2013}, month={Feb} }
 @article{singh_sethaphong_yingling_2011, title={Interactions of Cations with RNA Loop-Loop Complexes}, volume={101}, ISSN={["0006-3495"]}, url={https://publons.com/publon/5454556/}, DOI={10.1016/j.bpj.2011.06.033}, abstractNote={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.}, number={3}, journal={BIOPHYSICAL JOURNAL}, publisher={Elsevier BV}, author={Singh, Abhishek and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, year={2011}, month={Aug}, pages={727–735} }
 @article{sethaphong_singh_marlowe_yingling_2010, title={The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution}, volume={114}, ISSN={["1932-7455"]}, url={https://publons.com/publon/5454532/}, DOI={10.1021/jp906147q}, abstractNote={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.}, number={12}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, publisher={American Chemical Society (ACS)}, author={Sethaphong, Latsavongsakda and Singh, Abhishek and Marlowe, Ashley E. and Yingling, Yaroslava G.}, year={2010}, month={Apr}, pages={5506–5512} }