Search NASA⌕ Search

Engineering topics

Luo, Zhipu

Publications and source records attributed to Luo, Zhipu.

7 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Systematic Molecular Engineering of a Series of Aniline-Based Squaraine Dyes and Their Structure-Related Properties

With the objective of developing new near-infrared fluorescent probes and understanding the effect molecular structure exerts on physical properties, a series of aniline-based squaraine dyes with different number and position of methoxy substituents adjacent to the squaraine core were synthesized and investigated. Using both computational and experimental methods, we found that the subtle changes of the number or position of the methoxy substituents influenced the twisting angle of the structure and led to significant variations in optical properties. Moreover, the methoxy substituent also affected aggregation behavior due to steric effects. The X-ray crystal structure of one of the key members of the series, SD-2a, clearly demonstrates the distortion between the four-membered squaraine core and the adjacent aniline ring due to methoxy substitution. Structure-related fast relaxation processes were investigated by femtosecond pump–probe experiments and transient absorption spectra. Quantum chemical calculations and essential state models were exploited to analyze the primary experimental results. Here, the comprehensive investigation of structure-related properties of dihydroxylaniline-based squaraine dyes, with systematic substitution of OH by OCH 3 functional groups, serves as a guide for the design of novel squaraine dyes for photonics applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes

Tick-borne relapsing fever (RF) borreliosis is a neglected disease that is often misdiagnosed. RF species circulating in the United States include Borrelia turicatae, which is transmitted by argasid ticks. Environmental adaptation by RF Borrelia is poorly understood, however our previous studies indicated differential regulation of B. turicatae genes localized on the 150 kb linear megaplasmid during the tick-mammalian transmission cycle, including bta121. This gene is up-regulated by B. turicatae in the tick versus the mammal, and the encoded protein (BTA121) is predicted to be surface localized. The structure of BTA121 was solved by single-wavelength anomalous dispersion (SAD) using selenomethionine-derivative protein. The topology of BTA121 is unique with four helical domains organized into two helical bundles. Due to the sequence similarity of several genes on the megaplasmid, BTA121 can serve as a model for their tertiary structures. BTA121 has large interconnected tunnels and cavities that can accommodate ligands, notably long parallel helices, which have a large hydrophobic central pocket. Preliminary in-vitro studies suggest that BTA121 binds lipids, notably palmitate with a similar order of binding affinity as tablysin-15, a known palmitate-binding protein. The reported data will guide mechanistic studies to determine the role of BTA121 in the tick-mammalian transmission cycle of B. turicatae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Molecular Assembly-Induced Charge Transfer for Programmable Functionalities

The donor–acceptor interface within molecular charge transfer (CT) solids plays a vital role in the hybridization of molecular orbitals to determine their carrier transport and electronic delocalization. In this study reported herein, we demonstrate molecular assembly-driven bilayer and crystalline solids, consisting of electron donor dibenzotetrathiafulvalene (DBTTF) and acceptor C 60 , in which interfacial engineering-induced CT degree control is a key parameter for tuning its optical, electronic, and magnetic performance. Compared to the DBTTF/C 60 bilayer structure, the DBTTFC 60 cocrystalline solids show a stronger degree of charge transfer for broad CT absorption and a large dielectric constant. In addition, the DBTTFC 60 cocrystals exhibit distinct CT arrangement-driven anisotropic electron mobility and spin characteristics, which further enables the development of high-penetration and high-energy $γ$-ray photodetectors. The results presented in this paper provide a basis for the design and control of molecular charge transfer solids, which facilitates the integration of such materials into molecular electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2 duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinic P 2 1 lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Crystal Structure of MpPR-1i, a SCP/TAPS protein from Moniliophthora perniciosa, the fungus that causes Witches’ Broom Disease of Cacao

The pathogenic fungi Moniliophthora perniciosa causes Witches’ Broom Disease (WBD) of cacao. The structure of MpPR-1i, a protein expressed by M. perniciosa when it infects cacao, are presented. This is the first reported de novo structure determined by single-wavelength anomalous dispersion phasing upon soaking with selenourea. Each monomer has flexible loop regions linking the core alpha-beta-alpha sandwich topology that comprise ~50% of the structure, making it difficult to generate an accurate homology model of the protein. MpPR-1i is monomeric in solution but is packed as a high ~70% solvent content, crystallographic heptamer. The greatest conformational flexibility between monomers is found in loops exposed to the solvent channel that connect the two longest strands. MpPR-1i lacks the conserved CAP tetrad and is incapable of binding divalent cations. MpPR-1i has the ability to bind lipids, which may have roles in its infection of cacao. These lipids likely bind in the palmitate binding cavity as observed in tablysin-15, since MpPR-1i binds palmitate with comparable affinity as tablysin-15. Further studies are required to clarify the possible roles and underlying mechanisms of neutral lipid binding, as well as their effects on the pathogenesis of M. perniciosa so as to develop new interventions for WBD.

59 BASIC BIOLOGICAL SCIENCES↗