Molecular Virology: Virology laboratories
Research SummaryOur lab uses structural biology methods to study biological systems that have direct health impacts. A primary interest is innate immune systems, in particular, host cellular factors that fight viral infections such as those in the human body’s first line of defense against HIV. Another major interest is the mechanisms of fatty acid synthase (FAS), the cellular fat factory, and its close relationship to polyketide synthase (PKS), the cellular machinery that produces the most important natural products widely used in human medicine. Our goal is to provide a structural basis for understanding these systems and use the information gained to direct structure-based drug design of anti-viral, anti-fungal, and antibiotic compounds. Screening of inhibitors will be carried out at the Yale Chemical Genomics Screening Facility. Additionally, we are interested in the development of X-ray crystallographic methods that will push the limits of this technique.
Extensive Research Description
Our laboratory studies innate immune responses to viral infections and mechanisms of fatty acid synthesis. We use a variety of techniques, including X-ray crystallography, biochemistry, molecular biology, and computational biology. We also develop new X-ray crystallographic methods to facilitate the structural work.
Innate immune responses to HIV infection and viral countermeasures
APOBEC3 proteins. The innate immune system is the body's first line of defense against viral infections. Human antiviral protein APOBEC3G induces extensive mutations in HIV DNA that render the virus non-infectious. To evade the host defense system, HIV expresses the virion infectivity factor, Vif, which causes the degradation of APOBEC3G. We aim to establish the chemical and structural principles by which APOBEC3G mutates HIV DNA and the mechanisms by which HIV Vif sequesters APOBEC3G. Information gained from these studies will be used to direct structure-based design of Vif inhibitors that may lead to new anti-HIV drugs.
TRIM5a. Species-specific restriction factors can limit the number of host organisms that retroviruses are able to infect. The tripartite motif protein, TRIM5a, is an important component of the cross-species barrier to HIV and many other retroviruses. TRIM5a likely inhibits retrovirus infection through interactions with the viral capsid protein (CA). The goal of this project is to characterize the TRIM5a-CA interaction in vitro and establish the structural basis for this interaction.
Fatty acid synthesis
De novo synthesis of saturated fatty acids is catalyzed by fatty acid synthase (FAS) through multiple cycles of multi-step reactions. In yeast production of fatty acids is carried out by a 2.6 Megadalton FAS complex that contains 48 reaction centers. We have determined the crystal structure of the yeast FAS in the absence of any substrates. Additional reaction states will be examined to understand the mechanisms of fatty acid synthesis. Information gained can then be used to design FAS inhibitors that may lead to antifungal and obesity therapeutics.
X-ray crystallography at low resolutions
Electron microscope (EM) and X-ray crystallography. X-ray structure determination can utilize a low-resolution EM image for molecular replacement solution followed by phase extension to higher resolution by density modification.
Electron density deblurring. The electron density map obtained by X-ray crystallography or EM is often blurred due to motion and disorder in the crystal. We study the decoupling of the displacement by data sharpening techniques that treat individual domains of the molecule separately.
Folding calculation using X-ray data. Very low-resolution electron density maps (6-8 Å) can be used as a restraint for folding software in de novo calculations of atomic models.
Structure of a Prokaryotic Virtual Proton Pump at 3.2 Å Resolution
Fang, Y., Jayaram, H., Shane, T., Kolmakova-Partensky, L., Wu, F., Williams, C., Xiong. Y. & Miller. C. (2009). Structure of a Prokaryotic Virtual Proton Pump at 3.2 Å Resolution. Nature 460, 1040-1043.
A cytidine deaminase edits tRNAs in archaea
Randau, L*†, Stanley, B*, Kohlway, A., Mechta, S., Xiong, Y.† and Söll, D.† (2009) A cytidine deaminase edits tRNAs in archaea. Science 324, 657-659. (*: Equal contributions; †: Corresponding authors).
The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together
*Lomakin, I.B.,*#Xiong, Y., and #Steitz, T.A. (2007). The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell 129:319-332. (*equal contributions #corresponding authors).
Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template
Xiong, Y. and Steitz, T.A. (2004). Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430:640-645.
Structure of a synaptic ?d resolvase tetramer covalently linked to two cleaved DNAs
Li, W., Kamtekar, S., Xiong, Y., Grindley, N.D. and Steitz, T.A. Structure of a synaptic ?d resolvase tetramer covalently linked to two cleaved DNAs. Science 309, 1210-1215 (2005)
Full List of PubMed Publications
- Stoneham CA, Singh R, Jia X, Xiong Y, Guatelli J: Endocytic activity of HIV-1 Vpu: Phosphoserine-dependent interactions with clathrin adaptors. Traffic. 2017 Aug; 2017 Jun 27. PMID: 28504462
- Lu G, Xu Y, Zhang K, Xiong Y, Li H, Cui L, Wang X, Lou J, Zhai Y, Sun F, Zhang XC: Crystal structure of E. coli apolipoprotein N-acyl transferase. Nat Commun. 2017 Jul 4; 2017 Jul 4. PMID: 28885614
- Reiss CW, Xiong Y, Strobel SA: Structural Basis for Ligand Binding to the Guanidine-I Riboswitch. Structure. 2017 Jan 3; 2016 Dec 22. PMID: 28017522
- Nguyen HC, Wang W, Xiong Y: Cullin-RING E3 Ubiquitin Ligases: Bridges to Destruction. Subcell Biochem. 2017. PMID: 28271482
- Chen X, Yang K, Wu C, Chen C, Hu C, Buzovetsky O, Wang Z, Ji X, Xiong Y, Yang H: Mechanisms of activation and inhibition of Zika virus NS2B-NS3 protease. Cell Res. 2016 Nov; 2016 Oct 18. PMID: 27752039
- Antonucci JM, St Gelais C, de Silva S, Yount JS, Tang C, Ji X, Shepard C, Xiong Y, Kim B, Wu L: SAMHD1-mediated HIV-1 restriction in cells does not involve ribonuclease activity. Nat Med. 2016 Oct 6. PMID: 27711056
- Liang F, Longerich S, Miller AS, Tang C, Buzovetsky O, Xiong Y, Maranon DG, Wiese C, Kupfer GM, Sung P: Promotion of RAD51-Mediated Homologous DNA Pairing by the RAD51AP1-UAF1 Complex. Cell Rep. 2016 Jun 7; 2016 May 26. PMID: 27239033
- Patel N, Aldahmesh MA, Alkuraya H, Anazi S, Alsharif H, Khan AO, Sunker A, Al-Mohsen S, Abboud EB, Nowilaty SR, Alowain M, Al-Zaidan H, Al-Saud B, Alasmari A, Abdel-Salam GM, Abouelhoda M, Abdulwahab FM, Ibrahim N, Naim E, Al-Younes B, E AlMostafa A, AlIssa A, Hashem M, Buzovetsky O, Xiong Y, Monies D, Altassan N, Shaheen R, Al-Hazzaa SA, Alkuraya FS: Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies. Genet Med. 2016 Jun; 2015 Sep 10. PMID: 26355662
- Mahiti M, Toyoda M, Jia X, Kuang XT, Mwimanzi F, Mwimanzi P, Walker BD, Xiong Y, Brumme ZL, Brockman MA, Ueno T: Relative Resistance of HLA-B to Downregulation by Naturally Occurring HIV-1 Nef Sequences. MBio. 2016 Jan 19; 2016 Jan 19. PMID: 26787826
- Al-Yacoub N, Shaheen R, Awad SM, Kunhi M, Dzimiri N, Nguyen HC, Xiong Y, Al-Buraiki J, Al-Habeeb W, Alkuraya FS, Poizat C: FBXO32, encoding a member of the SCF complex, is mutated in dilated cardiomyopathy. Genome Biol. 2016 Jan 11; 2016 Jan 11. PMID: 26753747
- Shan H, Wang Z, Zhang F, Xiong Y, Yin CC, Sun F: A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules. Protein Cell. 2016 Jan; 2015 Dec 17. PMID: 26678751
- Tang C, Ji X, Wu L, Xiong Y: Impaired dNTPase activity of SAMHD1 by phosphomimetic mutation of Thr-592. J Biol Chem. 2015 Oct 30; 2015 Aug 20. PMID: 26294762
- Ji X, Xiong Y: Two tales (tails) of SAMHD1 destruction by Vpx. Cell Host Microbe. 2015 Apr 8. PMID: 25856752
- Jia X, Zhao Q, Xiong Y: HIV suppression by host restriction factors and viral immune evasion. Curr Opin Struct Biol. 2015 Apr; 2015 May 16. PMID: 25939065
- Nguyen HC, Yang H, Fribourgh JL, Wolfe LS, Xiong Y: Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex. Structure. 2015 Mar 3; 2015 Feb 5. PMID: 25661653
- Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA, Faqeih E, Alhashem A, Bashiri FA, Al-Owain M, Kentab AY, Sogaty S, Al Tala S, Temsah MH, Tulbah M, Aljelaify RF, Alshahwan SA, Seidahmed MZ, Alhadid AA, Aldhalaan H, AlQallaf F, Kurdi W, Alfadhel M, Babay Z, Alsogheer M, Kaya N, Al-Hassnan ZN, Abdel-Salam GM, Al-Sannaa N, Al Mutairi F, El Khashab HY, Bohlega S, Jia X, Nguyen HC, Hammami R, Adly N, Mohamed JY, Abdulwahab F, Ibrahim N, Naim EA, Al-Younes B, Meyer BF, Hashem M, Shaheen R, Xiong Y, Abouelhoda M, Aldeeri AA, Monies DM, Alkuraya FS: Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell Rep. 2015 Jan 13; 2014 Dec 31. PMID: 25558065
- Zhao Q, Xue X, Longerich S, Sung P, Xiong Y: Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer. Nat Commun. 2014 Dec 11; 2014 Dec 11. PMID: 25500724
- Fribourgh JL, Nguyen HC, Matreyek KA, Alvarez FJD, Summers BJ, Dewdney TG, Aiken C, Zhang P, Engelman A, Xiong Y: Structural insight into HIV-1 restriction by MxB. Cell Host Microbe. 2014 Nov 12; 2014 Oct 9. PMID: 25312384
- Patel N, El Mouzan MI, Al-Mayouf SM, Adly N, Mohamed JY, Al Mofarreh MA, Ibrahim N, Xiong Y, Zhao Q, Al-Saleem KA, Alkuraya FS: Study of Mendelian forms of Crohn's disease in Saudi Arabia reveals novel risk loci and alleles. Gut. 2014 Nov; 2014 Aug 21. PMID: 25147203
- Longerich S, Li J, Xiong Y, Sung P, Kupfer GM: Stress and DNA repair biology of the Fanconi anemia pathway. Blood. 2014 Oct 30; 2014 Sep 18. PMID: 25237197
- Ji X, Tang C, Zhao Q, Wang W, Xiong Y: Structural basis of cellular dNTP regulation by SAMHD1. Proc Natl Acad Sci U S A. 2014 Oct 14; 2014 Sep 29. PMID: 25267621
- Uchil PD, Pawliczek T, Reynolds TD, Ding S, Hinz A, Munro JB, Huang F, Floyd RW, Yang H, Hamilton WL, Bewersdorf J, Xiong Y, Calderwood DA, Mothes W: TRIM15 is a focal adhesion protein that regulates focal adhesion disassembly. J Cell Sci. 2014 Sep 15; 2014 Jul 11. PMID: 25015296
- Aldahmesh MA, Li Y, Alhashem A, Anazi S, Alkuraya H, Hashem M, Awaji AA, Sogaty S, Alkharashi A, Alzahrani S, Al Hazzaa SA, Xiong Y, Kong S, Sun Z, Alkuraya FS: IFT27, encoding a small GTPase component of IFT particles, is mutated in a consanguineous family with Bardet-Biedl syndrome. Hum Mol Genet. 2014 Jun 15; 2014 Jan 31. PMID: 24488770
- Shaheen R, Rahbeeni Z, Alhashem A, Faqeih E, Zhao Q, Xiong Y, Almoisheer A, Al-Qattan SM, Almadani HA, Al-Onazi N, Al-Baqawi BS, Saleh MA, Alkuraya FS: Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. Am J Hum Genet. 2014 Jun 5; 2014 May 15. PMID: 24836451
- Patel N, Khan AO, Mansour A, Mohamed JY, Al-Assiri A, Haddad R, Jia X, Xiong Y, Mégarbané A, Traboulsi EI, Alkuraya FS: Mutations in ASPH cause facial dysmorphism, lens dislocation, anterior-segment abnormalities, and spontaneous filtering blebs, or Traboulsi syndrome. Am J Hum Genet. 2014 May 1; 2014 Apr 24. PMID: 24768550
- Jia X, Weber E, Tokarev A, Lewinski M, Rizk M, Suarez M, Guatelli J, Xiong Y: Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1. Elife. 2014 Apr 29; 2014 Apr 29. PMID: 24843023
- Fribourgh JL, Nguyen HC, Wolfe LS, Dewitt DC, Zhang W, Yu XF, Rhoades E, Xiong Y: Core binding factor beta plays a critical role by facilitating the assembly of the Vif-cullin 5 E3 ubiquitin ligase. J Virol. 2014 Mar; 2014 Jan 3. PMID: 24390320
- Liu C, Xiong Y: Electron density sharpening as a general technique in crystallographic studies. J Mol Biol. 2014 Feb 20; 2013 Nov 21. PMID: 24269527
- Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei AR, Sung P, Xiong Y: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Nat Commun. 2014. PMID: 24390579
- Ji X, Wu Y, Yan J, Mehrens J, Yang H, DeLucia M, Hao C, Gronenborn AM, Skowronski J, Ahn J, Xiong Y: Mechanism of allosteric activation of SAMHD1 by dGTP. Nat Struct Mol Biol. 2013 Nov; 2013 Oct 20. PMID: 24141705
- Yang H, Ji X, Zhao G, Ning J, Zhao Q, Aiken C, Gronenborn AM, Zhang P, Xiong Y: Structural insight into HIV-1 capsid recognition by rhesus TRIM5α. Proc Natl Acad Sci U S A. 2012 Nov 6; 2012 Oct 22. PMID: 23091002
- Jia X, Singh R, Homann S, Yang H, Guatelli J, Xiong Y: Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef. Nat Struct Mol Biol. 2012 Jun 17; 2012 Jun 17. PMID: 22705789
- Kim J, Roberts A, Yuan H, Xiong Y, Anderson KS: Nucleocapsid protein annealing of a primer-template enhances (+)-strand DNA synthesis and fidelity by HIV-1 reverse transcriptase. J Mol Biol. 2012 Feb 3; 2011 Dec 23. PMID: 22210155
- Burton JL, Xiong Y, Solomon MJ: Mechanisms of pseudosubstrate inhibition of the anaphase promoting complex by Acm1. EMBO J. 2011 May 4; 2011 Apr 1. PMID: 21460798
- Butler EB, Xiong Y, Wang J, Strobel SA: Structural basis of cooperative ligand binding by the glycine riboswitch. Chem Biol. 2011 Mar 25. PMID: 21439473
- Pan B, Xiong Y, Steitz TA: How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA. Science. 2010 Nov 12. PMID: 21071662
- Yang H, Wang J, Jia X, McNatt MW, Zang T, Pan B, Meng W, Wang HW, Bieniasz PD, Xiong Y: Structural insight into the mechanisms of enveloped virus tethering by tetherin. Proc Natl Acad Sci U S A. 2010 Oct 26; 2010 Oct 12. PMID: 20940320
- Wolfe LS, Calabrese MF, Nath A, Blaho DV, Miranker AD, Xiong Y: Protein-induced photophysical changes to the amyloid indicator dye thioflavin T. Proc Natl Acad Sci U S A. 2010 Sep 28; 2010 Sep 8. PMID: 20826442
- Wolfe LS, Stanley BJ, Liu C, Eliason WK, Xiong Y: Dissection of the HIV Vif interaction with human E3 ubiquitin ligase. J Virol. 2010 Jul; 2010 May 12. PMID: 20463065
- Murphy JW, Yuan H, Kong Y, Xiong Y, Lolis EJ: Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family. Proteins. 2010 Apr. PMID: 20077567
- Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Söll D: A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science. 2009 May 1. PMID: 19407206
- Stanley BJ, Ehrlich ES, Short L, Yu Y, Xiao Z, Yu XF, Xiong Y: Structural insight into the human immunodeficiency virus Vif SOCS box and its role in human E3 ubiquitin ligase assembly. J Virol. 2008 Sep; 2008 Jun 18. PMID: 18562529
- Xiong Y: From electron microscopy to X-ray crystallography: molecular-replacement case studies. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 2007 Dec 5. PMID: 18094470
- Lomakin IB, Xiong Y, Steitz TA: The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell. 2007 Apr 20. PMID: 17448991
- Xiong Y, Steitz TA: A story with a good ending: tRNA 3'-end maturation by CCA-adding enzymes. Curr Opin Struct Biol. 2006 Feb; 2005 Dec 20. PMID: 16364630
- Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA: Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs. Science. 2005 Aug 19; 2005 Jun 30. PMID: 15994378
- Xiong Y, Steitz TA: Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature. 2004 Aug 5. PMID: 15295590
- Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L: Design of stable alpha-helical arrays from an idealized TPR motif. Structure. 2003 May. PMID: 12737816
- Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA: Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP. Cell. 2002 Dec 13. PMID: 12526808