@article{marlowe_singh_yingling_2012, title={The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study}, volume={32}, ISSN={["1873-0191"]}, url={https://publons.com/wos-op/publon/11561894/}, DOI={10.1016/j.msec.2012.07.044}, abstractNote={Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations.}, number={8}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, publisher={Elsevier BV}, author={Marlowe, Ashley E. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2012}, month={Dec}, pages={2583–2588} }
 @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} }