Structure-Based High-Throughput Epitope Analysis of Hexon Proteins in B and C Species Human Adenoviruses (HAdVs)

Human adenoviruses (HAdVs) are the etiologic agent of many human infectious diseases. The existence of at least 54 different serotypes of HAdVs has resulted in difficulties in clinical diagnosis. Acute respiratory tract disease (ARD) caused by some serotypes from B and C species is particularly serious. Hexon, the main coat protein of HAdV, contains the major serotype-specific B cell epitopes; however, few studies have addressed epitope mapping in most HAdV serotypes. In this study, we utilized a novel and rapid method for the modeling of homologous proteins based on the phylogenetic tree of protein families and built three-dimensional (3D) models of hexon proteins in B and C species HAdVs. Based on refined hexon structures, we used reverse evolutionary trace (RET) bioinformatics analysis combined with a specially designed hexon epitope screening algorithm to achieve high-throughput epitope mapping of all 13 hexon proteins in B and C species HAdVs. This study has demonstrated that all of the epitopes from the 13 hexon proteins are located in the proteins' tower regions; however, the exact number, location, and size of the epitopes differ among the HAdV serotypes

Stacked structure of the glycine dimer is more stable than the cyclic planar geometry with two O-H center dot center dot center dot O hydrogen bonds: Concerted action of empirical, high-level nonempirical ab initio, and experimental studies

The potential energy surface of the glycine dimer was investigated by the molecular dynamics/quenching method. A new empirical potential (EP1), largely based on the standard AMBER force field of Cornell et al. (Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M:; Spellmeyer, D. C.; Fox, T.; Caldwell, J. E.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179), was introduced. It employs atomic polarizabilities and RESP/B3LYP/aug-cc-pVTZ atomic charges and well mimics the high-level ab initio PES of the glycine dimer. Surprisingly, the most stable structure of the glycine dimer determined with the EP1 potential does not correspond to the planar cyclic structure with two O-H...O hydrogen bonds (C1) but to a stacked arrangement (S1). The stabilization energies of the 22 lowest-energy isomers of the glycine dimer were recalculated at the MP2/6-31G** level of theory, and the largest difference was found for the C1 and S1 structures. While the empirical potential favored the S1 structure by 3 kcal/mol, the correlated ab initio MP2/6-31G** calculations preferred the C1 structure by 2 kcal/mol. Applying higher levels of ab initio calculations (countrepoise corrected gradient optimization, larger basis sets, CCSD, CCSD(T), and QCISD(T) methods), we found that both structures are comparable in energy or that the stacked structure is even slightly more stable. The finding that the cyclic C1 structure is not the lowest energy configuration is in good agreement with IR spectroscopic studies on glycine dimers trapped in liquid helium droplets. All experimental spectra feature a strong absorption band in the region of the free O-H stretch, indicating that both hydroxyl groups cannot be hydrogen-bonded in the glycine dimer at the same time. Due to fast (subnanosecond) cooling of the glycine dimer in the helium droplets, it is also suggested that a T-shaped local minimum can be preserved in the cluster

RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%-94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database

An organometallic route to long helicenes

Along with the recent progress in the development of advanced synthetic methods, the chemical community has witnessed an increasing interest in promising carbon-rich materials. Among them, helicenes are unique 3D aromatic systems that are inherently chiral and attractive for asymmetric catalysis, chiral recognition and material science. However, there have been only limited attempts at synthesizing long helicenes, which represent challenging targets. Here, we report on an organometallic approach to the derivatives of undecacyclic helicene, which is based on intramolecular [2 + 2 + 2] cycloisomerization of aromatic hexaynes under metal catalysis closing 6 new cycles of a helicene backbone in a single operation. The preparation of nonracemic compounds relied on racemate resolution or diastereoselective synthesis supported by quantum chemical (density functional theory) calculations. The fully aromatic [11]helicene was studied in detail including the measurement and theoretical calculation of its racemization barrier and its organization on the InSb (001) surface by STM. This research provides a strategy for the synthesis of long helical aromatics that inherently comprise 2 possible channels for charge transport: Along a π-conjugated pathway and across an intramolecularly π-π stacked aromatic scaffold