This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Our research program is designed to utilize new types of macromolecular building blocks based on branched DNA, as the basis of specifically designed crystalline arrangements 3D structural motifs. The ultimate goals are to provide macromolecular scaffoldings, capable of binding, orienting and juxtaposing a variety of molecules, from biological macromolecules to organic conductors and optical memory components. We proposed and succeeded in determining structures of such a designed 3D system, the tensegrity triangle. This structure is a robust motif with three-fold rotational backbone symmetry, consisting of three helices that are directed in linearly independent directions, i.e., their helix axes do not all share the same plane. The helices are connected pair-wise by three Holliday-like crossover points, so as to produce an alternating over-and-under motif. Recently, we reported [Zheng et al. Nature 461, 74-77 (2009)] the X-ray crystal structure to 4 ? of a tensegrity triangle containing a single molecular species, comprised of three helical domains, each containing two double helical turns. Each triangle is centered on a vertex of a rhombohedron, creating a large cavity. Our more recent efforts have been directed in several different directions, all based on the structure of the published two-turn triangle. (A) We have been successful in increasing the numbers of helical turns in the triangle from 2 to 3 and 4 and in determining their crystal structures. While the refined structures all have the structural parameters predicted from their designs, the resolutions of the crystals obtained decrease with the increase in the number of helical turns. We are exploring the effect of changing the length of sticky ends that link the triangles, and also the impact of using natural DNA, rather than synthetic DNA, on the resolution of the crystals. (B) We are attempting to incorporate guest molecules into the internal cavities of the crystal structures;the cavities of the three structures with different length edges (2, 3 and 4 turns) are ~100 nm3, ~375 nm3 and ~1000 nm3. The guest species range from proteins, peptides, and peptidomimetics to dyes, metallic nanoparticles and segments of DNA. Isomorphous crystals have been obtained of such complexes both by co-crystallization and soaking. A report describing the crystal structure of a DNA crystal containing two distinct triangles programmed to crystallize according to the design is ready for submission. In addition, we have also demonstrated that the colors of the crystals can be controlled by the covalent attachment of dye molecules to the different molecules. As a rule our crystals are weakly diffracting, display a high degree of mosaicity and frequently appear in space group P1. Consequently the crystals require long exposure times, small oscillation angles and optimally data collection over 360 degrees.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1-BCMB-R (40))
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Brookhaven National Laboratory
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Fuller, Franklin D; Gul, Sheraz; Chatterjee, Ruchira et al. (2017) Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 14:443-449
Wangkanont, Kittikhun; Winton, Valerie J; Forest, Katrina T et al. (2017) Conformational Control of UDP-Galactopyranose Mutase Inhibition. Biochemistry 56:3983-3992
VanderLinden, Ryan T; Hemmis, Casey W; Yao, Tingting et al. (2017) Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. J Biol Chem 292:9493-9504
Song, Lingshuang; Yang, Lin; Meng, Jie et al. (2017) Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study. J Phys Chem Lett 8:347-351
Firestone, Ross S; Cameron, Scott A; Karp, Jerome M et al. (2017) Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase. ACS Chem Biol 12:464-473
Orlova, Natalia; Gerding, Matthew; Ivashkiv, Olha et al. (2017) The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators. Nucleic Acids Res 45:3724-3737
Ericson, Daniel L; Yin, Xingyu; Scalia, Alexander et al. (2016) Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase. J Lab Autom 21:107-14
Tajima, Nami; Karakas, Erkan; Grant, Timothy et al. (2016) Activation of NMDA receptors and the mechanism of inhibition by ifenprodil. Nature 534:63-8
Liu, Weifeng; Ramagopal, Udupi; Cheng, Huiyong et al. (2016) Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3. Structure 24:2016-2023
Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira et al. (2016) Structure of photosystem II and substrate binding at room temperature. Nature 540:453-457

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