@article{taliercio_allen_essenberg_klueva_nguyen_patil_payton_millena_phillips_pierce_et al._2006, title={Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs}, volume={49}, ISSN={["1480-3321"]}, DOI={10.1139/G05-115}, abstractNote={ In an effort to expand the Gossypium hirsutum L. (cotton) expressed sequence tag (EST) database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in the EST database (dbEST, GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely differentially expressed in stems, cotyledons, and drought-stressed tissues. Annotation of the differentially expressed cDNAs tentatively identified genes involved in lignin metabolism, starch biosynthesis and stress response, consistent with pathways likely to be active in the tissues under investigation. Simple sequence repeats (SSRs) were identified among these ESTs, and an inexpensive method was developed to screen genomic DNA for the presence of these SSRs. At least 69 SSRs potentially useful in mapping were identified. Selected amplified SSRs were isolated and sequenced. The sequences corresponded to the EST containing the SSRs, confirming that these SSRs will potentially map the gene represented by the EST. The ESTs containing SSRs were annotated to help identify the genes that may be mapped using these markers.Key words: drought stress, gene annotation, gene mapping, tentative consensus sequence (TC), Xanthomonas campestris. }, number={4}, journal={GENOME}, author={Taliercio, Earl and Allen, Randy D. and Essenberg, Margaret and Klueva, Natalya and Nguyen, Henry and Patil, Mohini A. and Payton, Paxton and Millena, Ana Cecilia M. and Phillips, Angela L. and Pierce, Margaret L. and et al.}, year={2006}, month={Apr}, pages={306–319} }
 @misc{nguyen_hall_2006, title={Spontaneous fibril formation by polyalanines; Discontinuous molecular dynamics simulations}, volume={128}, ISSN={["1520-5126"]}, DOI={10.1021/ja0539140}, abstractNote={Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.}, number={6}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Nguyen, HD and Hall, CK}, year={2006}, month={Feb}, pages={1890–1901} }
 @article{nguyen_hall_2005, title={Kinetics of fibril formation by polyalanine peptides}, volume={280}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M407338200}, abstractNote={Ordered β-sheet complexes, termed amyloid fibrils, are the underlying structural components of the intra- and extracellular fibrillar protein deposits that are associated with a variety of human diseases, including Alzheimer's, Parkinson's, and the prion diseases. In this work, we investigated the kinetics of fibril formation using our newly developed off-lattice intermediate resolution model, PRIME. The model is simple enough to allow the treatment of large multichain systems while maintaining a fairly realistic description of protein dynamics without built-in bias toward any conformation when used in conjunction with constant temperature discontinuous molecular dynamics, a fast alternative to conventional molecular dynamics. Simulations were performed on systems containing 48–96 model Ac-KA14K-NH2 peptides. We found that fibril formation for polyalanines incorporate features that are characteristic of three models, the templated assembly, nucleated polymerization, and nucleated conformational conversion models, but that none of them gave a completely satisfactory description of the simulation kinetics. Fibril formation was nucleation-dependent, occurring after a lag time that decreased with increasing peptide concentration and increased with increasing temperature. Fibril formation appeared to be a conformational conversion process in which small amorphous aggregates → β-sheets → ordered nucleus → subsequent rapid growth of a small stable fibril or protofilament. Fibril growth in our simulations involved both β-sheet elongation, in which the fibril grew by adding individual peptides to the end of each β-sheet, and lateral addition, in which the fibril grew by adding already formed β-sheets to its side. The initial rate of fibril formation increased with increasing concentration and decreased with increasing temperature.}, number={10}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Nguyen, HD and Hall, CK}, year={2005}, month={Mar}, pages={9074–9082} }
 @article{nguyen_hall_2004, title={Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0407273101}, abstractNote={Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. We report molecular-level simulation of spontaneous fibril formation. Systems containing 12-96 model polyalanine peptides form fibrils at temperatures greater than a critical temperature that decreases with peptide concentration and exceeds the peptide's folding temperature, consistent with experimental findings. Formation of small amorphous aggregates precedes ordered nucleus formation and subsequent rapid fibril growth through addition of β-sheets laterally and monomeric peptides at fibril ends. The fibril's structure is similar to that observed experimentally.}, number={46}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Nguyen, HD and Hall, CK}, year={2004}, month={Nov}, pages={16180–16185} }
 @article{nguyen_hall_2004, title={Phase diagrams describing fibrillization by polyalanine peptides}, volume={87}, ISSN={["1542-0086"]}, DOI={10.1529/biophysj.104.047159}, abstractNote={Amyloid fibrils are the structural components underlying the intra- and extracellular protein deposits that are associated with a variety of human diseases, including Alzheimer's, Parkinson's, and the prion diseases. In this work, we examine the thermodynamics of fibril formation using our newly-developed off-lattice intermediate-resolution protein model, PRIME. The model is simple enough to allow the treatment of large multichain systems while maintaining a fairly realistic description of protein dynamics when used in conjunction with constant-temperature discontinuous molecular dynamics, a fast alternative to conventional molecular dynamics. We conduct equilibrium simulations on systems containing 96 Ac-KA14K-NH2 peptides over a wide range of temperatures and peptide concentrations using the replica-exchange method. Based on measured values of the heat capacity, radius of gyration, and percentage of peptides that form the various structures, a phase diagram in the temperature-concentration plane is constructed delineating the regions where each structure is stable. There are four distinct single-phase regions: alpha-helices, fibrils, nonfibrillar beta-sheets, and random coils; and four two-phase regions: random coils/nonfibrillar beta-sheets, random coils/fibrils, fibrils/nonfibrillar beta-sheets, and alpha-helices/nonfibrillar beta-sheets. The alpha-helical region is at low temperature and low concentration. The nonfibrillar beta-sheet region is at intermediate temperatures and low concentrations and expands to higher temperatures as concentration is increased. The fibril region occurs at intermediate temperatures and intermediate concentrations and expands to lower as the peptide concentration is increased. The random-coil region is at high temperatures and all concentrations; this region shifts to higher temperatures as the concentration is increased.}, number={6}, journal={BIOPHYSICAL JOURNAL}, author={Nguyen, HD and Hall, CK}, year={2004}, month={Dec}, pages={4122–4134} }
 @article{nguyen_marchut_hall_2004, title={Solvent effects on the conformational transition of a model polyalanine peptide}, volume={13}, ISSN={0961-8368}, url={http://dx.doi.org/10.1110/ps.04701304}, DOI={10.1110/ps.04701304}, abstractNote={Abstract}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Nguyen, Hung D. and Marchut, Alexander J. and Hall, Carol K.}, year={2004}, month={Dec}, pages={2909–2924} }
 @article{nguyen_hall_2002, title={Effect of rate of chemical or thermal renaturation on refolding and aggregation of a simple lattice protein}, volume={80}, ISSN={["1097-0290"]}, DOI={10.1002/bit.10448}, abstractNote={Abstract}, number={7}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Nguyen, HD and Hall, CK}, year={2002}, month={Dec}, pages={823–834} }