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1. Supramolecular porphyrinic prisms: coordinative assembly and solution phase X-ray structural characterization

Author:
Zuo, Xiaobing,   et al.   ; Lee, Suk Joong; Mulfort, Karen L.; O'Donnell, Jodi L.; Goshe, Andrew J.; Wesson, Paul J.; Nguyen, SonBinh T.; Hupp, Joseph T.; Tiede, David M.;     Show all 9 Authors
Source:
Chemical communications 2006 no.44 pp. 4581-4583
ISSN:
1364-548X
Subject:
X-radiation; X-ray diffraction; chemical reactions; nuclear magnetic resonance spectroscopy; porphyrins; prisms
Abstract:
... Supramolecular porphyrin prisms have been obtained via coordinative self-assembly and characterized by ¹H NMR, PFG NMR, electronic absorption spectroscopy and synchrotron-based measurements of solution phase X-ray scattering and diffraction. ...
DOI:
10.1039/b610025b

2. X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis

Author:
Zuo, Xiaobing,   et al.   ; Tiede, David M.; Mardis, Kristy L.;     Show all 3 Authors
Source:
Photosynthesis research 2009 v.102 no.2-3 pp. 267-279
ISSN:
0166-8595
Subject:
X-radiation; chemical structure; detectors; energy conversion; photosynthesis; solar energy
Abstract:
... Advances in X-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining X-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for X-ray scattering are discussed and illustrated with selected examples demonstrating the ability to ...
DOI:
10.1007/s11120-009-9475-6
PubMed:
19636808
PubMed Central:
PMC2891609

3. Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus

Author:
Zuo, Xiaobing,   et al.   ; Wang, Jinbu; Yu, Ping; Eyler, Dan; Xu, Huan; Starich, Mary R.; Tiede, David M.; Simon, Anne E.; Kasprzak, Wojciech; Schwieters, Charles D.; Shapiro, Bruce A.; Wang, Yun-Xing;     Show all 12 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2010 v.107 no.4 pp. 1385-1390
ISSN:
0027-8424
Subject:
nuclear magnetic resonance spectroscopy; X-ray diffraction; Turnip crinkle virus; ribosomes; binding sites; 3' untranslated regions; molecular conformation
Abstract:
... The 3' untranslated region (3' UTR) of turnip crinkle virus (TCV) genomic RNA contains a cap-independent translation element (CITE), which includes a ribosome-binding structural element (RBSE) that participates in recruitment of the large ribosomal subunit. In addition, a large symmetric loop in the RBSE plays a key role in coordinating the incompatible processes of viral translation and replicati ...
DOI:
10.1073/pnas.0908140107
PubMed:
20080629
PubMed Central:
PMC2803139

4. Two ZnF-UBP Domains in Isopeptidase T (USP5)

Author:
Zuo, Xiaobing,   et al.   ; Avvakumov, George V.; Walker, John R.; Xue, Sheng; Allali-Hassani, Abdellah; Asinas, Abdalin; Nair, Usha B.; Fang, Xianyang; Wang, Yun-Xing; Wilkinson, Keith D.; Dhe-Paganon, Sirano;     Show all 11 Authors
Source:
Biochemistry 2012 v.51 no.6 pp. 1188-1198
ISSN:
1520-4995
Subject:
active sites; catalytic activity; cysteine proteinases; enzyme activation; humans; hydrolysis; ubiquitin
Abstract:
... Human ubiquitin-specific cysteine protease 5 (USP5, also known as ISOT and isopeptidase T), an 835-residue multidomain enzyme, recycles ubiquitin by hydrolyzing isopeptide bonds in a variety of unanchored polyubiquitin substrates. Activation of the enzyme’s hydrolytic activity toward ubiquitin-AMC (7-amino-4-methylcoumarin), a fluorogenic substrate, by the addition of free, unanchored monoubiquiti ...
DOI:
10.1021/bi200854q

5. Self-Recognition of Structurally Identical, Rod-Shaped Macroions with Different Central Metal Atoms during Their Assembly Process

Author:
Zuo, Xiaobing,   et al.   ; Yin, Panchao; Zhang, Jin; Li, Tao; Hao, Jian; Warner, Anna Marie; Chattopadhyay, Soma; Shibata, Tomohiro; Wei, Yongge; Liu, Tianbo;     Show all 10 Authors
Source:
Journal of the American Chemical Society 2013 v.135 no.11 pp. 4529-4536
ISSN:
1520-5126
Subject:
activation energy; chemical elements; dissociation; electrostatic interactions; encapsulation; energy-dispersive X-ray analysis; transmission electron microscopy
Abstract:
... Two rod-shaped macroanions, ((C₄H₉)₄N)₇[Mo₆O₁₈NC(OCH₂)₃XMo₆O₁₈(OCH₂)₃CNMo₆O₁₈] (X = Mnᴵᴵᴵ (1), Feᴵᴵᴵ (2)), with almost identical charge densities and morphologies except for their different encapsulated central metal atoms were each observed to self-assemble into “blackberry”-type supramolecular structures in their dilute solution, driven by the counterion-mediated attraction. Amazingly, the two m ...
DOI:
10.1021/ja400656j

6. Exploring the Programmable Assembly of a Polyoxometalate–Organic Hybrid via Metal Ion Coordination

Author:
Zuo, Xiaobing,   et al.   ; Yin, Panchao; Li, Tao; Forgan, Ross S.; Lydon, Claire; Zheng, Zhaoxiong Norm; Lee, Byeongdu; Long, Deliang; Cronin, Leroy; Liu, Tianbo;     Show all 10 Authors
Source:
Journal of the American Chemical Society 2013 v.135 no.36 pp. 13425-13432
ISSN:
1520-5126
Subject:
EDTA (chelating agent); cations; dimethyl sulfoxide; hybrids; light scattering; metal ions; nuclear magnetic resonance spectroscopy; zinc
Abstract:
... The conformational flexibility and programmed assembly of a dumbbell-shaped polyoxometalate–organic hybrid molecule comprising two Dawson-type polyoxometalates linked by a 2,2′-bipyridine unit, which can be coordinate to metal ions, in this case of Zn²⁺, are described. SAXS, UV/vis, and NMR spectroscopic techniques confirm that the hybrid molecules exist as the trans dumbbell in metal-ion-free sol ...
DOI:
10.1021/ja404777g

7. Self-Assembly of Rodlike Virus to Superlattices

Author:
Zuo, Xiaobing,   et al.   ; Li, Tao; Zan, Xingjie; Sun, Yong; Li, Xiaodong; Senesi, Andrew; Winans, Randall E.; Wang, Qian; Lee, Byeongdu;     Show all 9 Authors
Source:
Langmuir 2013 v.29 no.41 pp. 12777-12784
ISSN:
1520-5827
Subject:
Tobacco mosaic virus; X-radiation; aqueous solutions; bacteriophages; entropy; methylcellulose; nanoparticles; polymers; sodium chloride; temperature; transmission electron microscopy
Abstract:
... Rodlike tobacco mosaic virus (TMV) has been found to assemble into superlattices in aqueous solution using the polymer methylcellulose to induce depletion and free volume entropy-based attractive forces. Both transmission electron microscopy and small-angle X-ray scattering show that the superlattices form in both semidilute and concentrated regimes of polymer, where the free volume entropy and th ...
DOI:
10.1021/la402933q

8. Rational Design of Helical Nanotubes from Self-Assembly of Coiled-Coil Lock Washers

Author:
Zuo, Xiaobing,   et al.   ; Xu, Chunfu; Liu, Rui; Mehta, Anil K.; Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R.; Dunin-Horkawicz, Stanislaw; Morris, Kyle; Serpell, Louise C.; Wall, Joseph S.; Conticello, Vincent P.;     Show all 11 Authors
Source:
Journal of the American Chemical Society 2013 v.135 no.41 pp. 15565-15578
ISSN:
1520-5126
Subject:
amino acid sequences; binding capacity; crystal structure; fluorescence; fluorescent dyes; mutagenesis; nanotubes
Abstract:
... Design of a structurally defined helical assembly is described that involves recoding of the amino acid sequence of peptide GCN4-pAA. In solution and the crystalline state, GCN4-pAA adopts a 7-helix bundle structure that resembles a supramolecular lock washer. Structurally informed mutagenesis of the sequence of GCN4-pAA afforded peptide 7HSAP1, which undergoes self-association into a nanotube via ...
DOI:
10.1021/ja4074529

9. An Unusual Topological Structure of the HIV-1 Rev Response Element

Author:
Zuo, Xiaobing,   et al.   ; Fang, Xianyang; Wang, Jinbu; O’Carroll, Ina P.; Mitchell, Michelle; Wang, Yi; Yu, Ping; Liu, Yu; Rausch, Jason W.; Dyba, Marzena A.; Kjems, Jørgen; Schwieters, Charles D.; Seifert, Soenke; Winans, Randall E.; Watts, Norman R.; Stahl, Stephen J.; Wingfield, Paul T.; Byrd, R. Andrew; Le Grice, Stuart F.J.; Rein, Alan; Wang, Yun-Xing;     Show all 21 Authors
Source:
Cell 2013 v.155 pp. 594-605
ISSN:
0092-8674
Subject:
Human immunodeficiency virus 1; binding sites; legs; messenger RNA; physiological transport; topology; viruses
Abstract:
... Nuclear export of unspliced and singly spliced viral mRNA is a critical step in the HIV life cycle. The structural basis by which the virus selects its own mRNA among more abundant host cellular RNAs for export has been a mystery for more than 25 years. Here, we describe an unusual topological structure that the virus uses to recognize its own mRNA. The viral Rev response element (RRE) adopts an “ ...
DOI:
10.1016/j.cell.2013.10.008
PubMed:
24243017
PubMed Central:
PMC3918456

10. Assembly and Distributive Action of an Archaeal DNA Polymerase Holoenzyme

Author:
Zuo, Xiaobing,   et al.   ; Bauer, Robert J.; Wolff, Ian D.; Lin, Hsiang-Kai; Trakselis, Michael A.;     Show all 5 Authors
Source:
Journal of Molecular Biology 2013 v.425 pp. 4820-4836
ISSN:
0022-2836
Subject:
DNA; DNA replication; DNA-directed DNA polymerase; Sulfolobus solfataricus; X-radiation; adenosine triphosphate; dissociation; energy transfer; fluorescence; hydrolysis; models; proliferating cell nuclear antigen
Abstract:
... The assembly and enzymatic ability of the replication DNA polymerase holoenzyme from Sulfolobus solfataricus (Sso) was investigated using presteady-state fluorescence resonance energy transfer assays coupled with functional and structural studies. Kinetic experiments reveal that ATP binding to replication factor C (RFC) is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nucle ...
DOI:
10.1016/j.jmb.2013.09.003
PubMed:
24035812

11. Structurally Defined Nanoscale Sheets from Self-Assembly of Collagen-Mimetic Peptides

Author:
Zuo, Xiaobing,   et al.   ; Jiang, Tao; Xu, Chunfu; Liu, Yang; Liu, Zheng; Wall, Joseph S.; Lian, Tianquan; Salaita, Khalid; Ni, Chaoying; Pochan, Darrin; Conticello, Vincent P.;     Show all 11 Authors
Source:
Journal of the American Chemical Society 2014 v.136 no.11 pp. 4300-4308
ISSN:
1520-5126
Subject:
collagen; electrostatic interactions; nanosheets; peptides
Abstract:
... We report the design of two collagen-mimetic peptide sequences, NSI and NSII, that self-assemble into structurally defined nanoscale sheets. The underlying structure of these nanosheets can be understood in terms of the layered packing of collagen triple helices in two dimensions. These nanosheet assemblies represent a novel morphology for collagen-based materials, which, on the basis of their def ...
DOI:
10.1021/ja412867z

12. Super-Stable, Highly Monodisperse Plasmonic Faradaurate-500 Nanocrystals with 500 Gold Atoms: Au∼500(SR)∼120

Author:
Zuo, Xiaobing,   et al.   ; Kumara, Chanaka; Ilavsky, Jan; Chapman, Karena W.; Cullen, David A.; Dass, Amala;     Show all 6 Authors
Source:
Journal of the American Chemical Society 2014 v.136 no.20 pp. 7410-7417
ISSN:
1520-5126
Subject:
X-radiation; gold; mass spectrometry; nanocrystals; nanogold; nanoparticles; transmission electron microscopy
Abstract:
... Determining the composition of plasmonic nanoparticles is challenging due to a lack of tools to accurately quantify the number of atoms within the particle. Mass spectrometry plays a significant role in determining the nanoparticle composition at the atomic level. Significant progress has been made in understanding ultrasmall gold nanoparticles such as Au₂₅(SR)₁₈ and Au₃₈(SR)₂₄, which have Au core ...
DOI:
10.1021/ja502327a

13. Relationship between Interchain Interaction, Exciton Delocalization, and Charge Separation in Low-Bandgap Copolymer Blends

Author:
Zuo, Xiaobing,   et al.   ; Guo, Zhi; Lee, Doyun; Schaller, Richard D.; Lee, Byeongdu; Luo, TengFei; Gao, Haifeng; Huang, Libai;     Show all 8 Authors
Source:
Journal of the American Chemical Society 2014 v.136 no.28 pp. 10024-10032
ISSN:
1520-5126
Subject:
composite polymers; crystal structure; energy; photovoltaic cells; spectroscopy
Abstract:
... We present a systematic study of the roles of crystallinity, interchain interaction, and exciton delocalization on ultrafast charge separation pathways in donor–acceptor copoloymer blends. We characterize the energy levels, excited state structures, and dynamics of the interchain species by combined ultrafast spectroscopy and computational quantum chemistry approaches. The alkyl side chain of a hi ...
DOI:
10.1021/ja503465s

14. Crystal structure of triple-BRCT-domain of ECT2 and insights into the binding characteristics to CYK-4

Author:
Zuo, Xiaobing,   et al.   ; Zou, Yang; Shao, Zhenhua; Peng, Junhui; Li, Fudong; Gong, Deshun; Wang, Chongyuan; Zhang, Zhiyong; Wu, Jihui; Shi, Yunyu; Gong, Qingguo;     Show all 11 Authors
Source:
FEBS letters 2014 v.588 pp. 2911-2920
ISSN:
0014-5793
Subject:
Homo sapiens; anaphase; binding properties; crystal structure; cytokinesis; interphase
Abstract:
... Homo sapiens ECT2 is a cell cycle regulator that plays critical roles in cytokinesis. ECT2 activity is restrained during interphase via intra-molecular interactions that involve its N-terminal triple-BRCT-domain and its C-terminal DH–PH domain. At anaphase, this self-inhibitory mechanism is relieved by Plk1-phosphorylated CYK-4, which directly engages the ECT2 BRCT domain. To provide a structural ...
DOI:
10.1016/j.febslet.2014.07.019

15. Solid-to-fluid–like DNA transition in viruses facilitates infection

Author:
Zuo, Xiaobing,   et al.   ; Liu, Ting; Sae-Ueng, Udom; Li, Dong; Lander, Gabriel C.; Jönsson, Bengt; Rau, Donald; Shefer, Ivetta; Evilevitch, Alex;     Show all 9 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2014 v.111 no.41 pp. 14675-14680
ISSN:
0027-8424
Subject:
DNA; Escherichia coli; bacteriophages; capsid; genome; humans; virus replication
Abstract:
... Releasing the packaged viral DNA into the host cell is an essential process to initiate viral infection. In many double-stranded DNA bacterial viruses and herpesviruses, the tightly packaged genome is hexagonally ordered and stressed in the protein shell, called the capsid. DNA condensed in this state inside viral capsids has been shown to be trapped in a glassy state, with restricted molecular mo ...
DOI:
10.1073/pnas.1321637111
PubMed:
25271319
PubMed Central:
PMC4205597

16. Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

Author:
Zuo, Xiaobing,   et al.   ; Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Noll, Bruce C.;     Show all 10 Authors
Source:
Journal of the American Chemical Society 2015 v.137 no.14 pp. 4610-4613
ISSN:
1520-5126
Subject:
X-radiation; X-ray diffraction; crystal structure; electrochemistry; electrospray ionization mass spectrometry; gold; ligands; nanomaterials; surface plasmon resonance
Abstract:
... Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the “nanostructure problem”. Here, by using rigid and bulky ligands, we have overcome this limitation and success ...
DOI:
10.1021/ja513152h

17. Rational Design of Multilayer Collagen Nanosheets with Compositional and Structural Control

Author:
Zuo, Xiaobing,   et al.   ; Jiang, Tao; Vail, Owen A.; Jiang, Zhigang; Conticello, Vincent P.;     Show all 5 Authors
Source:
Journal of the American Chemical Society 2015 v.137 no.24 pp. 7793-7802
ISSN:
1520-5126
Subject:
calcium; collagen; electrostatic interactions; image analysis; microscopy; nanoparticles; nanosheets; peptides; zeta potential
Abstract:
... Two collagen-mimetic peptides, CP⁺ and CP–, are reported in which the sequences comprise a multiblock architecture having positively charged N-terminal (Pro-Arg-Gly)₃ and negatively charged C-terminal (Glu-Hyp-Gly)₃ triad extensions, respectively. CP⁺ rapidly self-associates into positively charged nanosheets based on a monolayer structure. In contrast, CP– self-assembles to form negatively charge ...
DOI:
10.1021/jacs.5b03326

18. New Class of Heterogeneous Helical Peptidomimetics

Author:
Zuo, Xiaobing,   et al.   ; Wu, Haifan; Qiao, Qiao; Teng, Peng; Hu, Yaogang; Antoniadis, Dimitrios; Cai, Jianfeng;     Show all 7 Authors
Source:
Organic letters 2015 v.17 no.14 pp. 3524-3527
ISSN:
1523-7052
Subject:
X-radiation; amino acids; chemical reactions; chemical structure; circular dichroism spectroscopy; nuclear magnetic resonance spectroscopy; organic compounds; peptides; temperature
Abstract:
... A new class of unnatural heterogeneous foldamers is reported to contain alternative α-amino acid and sulfono-γ-AA amino acid residues in a 1:1 repeat pattern. Two-dimensional NMR data show that two 1:1 α/sulfono-γ-AA peptides with diverse side chains form analogous right-handed helical structures in solution. The effects of sequence length, side chain, N-capping, and temperature on folding propens ...
DOI:
10.1021/acs.orglett.5b01608

19. Homogeneous and Heterogeneous (Fex, Cr1–x)(OH)3 Precipitation: Implications for Cr Sequestration

Author:
Zuo, Xiaobing,   et al.   ; Dai, Chong; Cao, Bo; Hu, Yandi;     Show all 4 Authors
Source:
Environmental Science & Technology 2016 v.50 no.4 pp. 1741-1749
ISSN:
1520-5851
Subject:
X-radiation; aquatic environment; chemical composition; chromium; iron; nanoparticles; pH; quartz
Abstract:
... The formation of (Fe, Cr)(OH)₃ nanoparticles determines the fate of aqueous Cr in many aquatic environments. Using small-angle X-ray scattering, precipitation rates of (Fe, Cr)(OH)₃ nanoparticles in solution and on quartz were quantified from 0.1 mM Fe(III) solutions containing 0–0.25 mM Cr(III) at pH = 3.7 ± 0.2. Concentration ratio of aqueous Cr(III)/Fe(III) controlled the chemical composition ( ...
DOI:
10.1021/acs.est.5b04319

20. Impact of Interfacial Roughness on the Sorption Properties of Nanocast Polymers

Author:
Zuo, Xiaobing,   et al.   ; Sridhar, Manasa; Gunugunuri, Krishna R.; Hu, Naiping; Motahari, Ahmad; Schaefer, Dale W.; Thiel, Stephen W.; Smirniotis, Panagiotis G.;     Show all 8 Authors
Source:
Macromolecules 2016 v.49 no.7 pp. 2663-2670
ISSN:
1520-5835
Subject:
X-ray diffraction; foams; fractal dimensions; lysozyme; models; nitrogen; polymers; roughness; small-angle X-ray scattering; sorption; sorption isotherms; transmission electron microscopy
Abstract:
... Nanocasting is an emerging method to prepare organic polymers with regular, nanometer pores using inorganic templates. This report assesses the impact of imperfect template replication on the sorption properties of such polymer castings. Existing X-ray diffraction data show that substantial diffuse scattering exists in the small-angle region even though TEM images show near perfect lattices of uni ...
DOI:
10.1021/acs.macromol.6b00304