2018

29.5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.

Peng Y., McCorvy J.D., Harpsøe K., Lansu K., Yuan S., Popov P., Qu L., Pu M., Che T., Nikolajsen L.F., Huang X.P., Wu Y., Shen L., Bjørn-Yoshimoto W.E., Ding K., Wacker D., Han G.W., Cheng J., Katritch V., Jensen A.A., Hanson M.A., Zhao S., Gloriam D.E., Roth B.L.*, Stevens R.C.*, Liu Z.J.*, 5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology Cell. 2018 Jan 19. pii: S0092-8674(18)30001-1

28.Prediction of enzymatic pathways by integrative pathway mapping.

Calhoun, S.; Korczynska, M.; Wichelecki, D. J.; San Francisco, B.; Zhao, S.; Rodionov, D. A.; Vetting, M. W.; Al-Obaidi, N. F.; Lin, H.; O'Meara, M. J.; Scott, D. A.; Morris, J. H.; Russel, D.; Almo, S. C.; Osterman, A. L.; Gerlt, J. A.*; Jacobson, M. P.*; Shoichet, B. K.*; Sali, A.*, Prediction of enzymatic pathways by integrative pathway mapping.Elife. 2018 Jan 29;7. pii: e31097.

2017

27.Structural insights into the committed step of bacterial phospholipid biosynthesis.

Li,Z.; Tang,Y.; Wu,Y.; Zhao,S.; Bao,J.; Luo,Y.; Li,D.*, Structural insights into the committed step of bacterial phospholipid biosynthesis.Nat Commun.2017 Nov 22;8(1):1691.

26.Crystal structures of agonist-bound human cannabinoid receptor CB1.

Hua, T.; Vemuri, K.; Nikas, S.; Laprairie, R. B.; Wu, Y.; Qu, L.; Pu, M.; Korde, A.; Shan J.; Ho, J. H.; Han, G. W.; Ding, K.; Li X.; Liu H.; Hanson, M. A.; Zhao, S.*; Bohn, L. M.*; Makriyannis, A.*; Stevens, R. C.; Liu, Z. J.*, Crystal structures of agonist-bound human cannabinoid receptor CB1. Nature. 2017 Jul 27;547(7664):468-471.[Membrane Protein]

25.A Novel Lid-Covering Peptide Inhibitor of Nicotinic Acetylcholine Receptors Derived from αD-Conotoxin GeXXA.

Yang, L.; Tae, H.-S.; Fan, Z.; Shao, X.; Xu, S.; Zhao, S.; Adams, D.*; Wang, C.*, A Novel Lid-Covering Peptide Inhibitor of Nicotinic Acetylcholine Receptors Derived from αD-Conotoxin GeXXA. Mar Drugs. 2017 Jun 5;15(6).pii:E164.[Membrane Protein]

24.Structural Basis for Apelin Control of the Human Apelin Receptor.

Ma, Y.; Yue, Y.; Ma, Y.; Zhang, Q.; Zhou, Q.; Song, Y.; Shen, Y.; Li, X.; Ma, X.; Li, C.; Hanson, M. A.; Han, G. W.; Sickmier, E. A.; Swaminath, G.; Zhao, S.; Stevens, R. C.; Hu, L. A.; Zhong, W.; Zhang, M.; Xu, F.*, Structural Basis for Apelin Control of the Human Apelin Receptor. Structure. 2017 Jun 6;25(6):858-866.[Membrane Protein]

23.Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.

Song, G.; Yang, D.; Wang, Y.; de Graaf, C.; Zhou, Q.; Jiang, S.; Liu, K.; Cai, X.; Dai, A.; Lin, G.; Liu, D.; Wu, F.; Wu, Y.; Zhao, S.; Ye, L.; Han, G. W.; Lau, J.; Wu, B.; Hanson, M. A.; Liu, Z.J.*; Wang, M.W.*; Stevens, R. C.*, Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Nature. 2017 Jun 8;546(7657):312-315.[Membrane Protein]

22.Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand.

Zhang, X.; Zhao, F.; Wu, Y.; Yang, J.; Han, G. W.; Zhao, S.; Ishchenko, A.; Ye, L.; Lin, X.; Ding, K.; Dharmarajan, V.; Griffin, P. R.; Gati, C.; Nelson, G.; Hunter, M. S.; Hanson, M. A.; Cherezov, V.; Stevens, R. C.; Tan, W.*; Tao, H.*; Xu, F.*, Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nat Commun. 2017 May 17;8:15383.[Membrane Protein]

21.A structurally guided dissection-then-evolution strategy for ligand optimization of smoothened receptor.

Ye, L.;Ding, K.; Zhao, F.; Liu, X.; Wu, Y.; Liu, Y.; Xue, D.; Zhou, F.; Zhang, X.; Stevens, R. C.; Xu, F.; Zhao, S.*; Tao, H.*, A structurally guided dissection-then-evolution strategy for ligand optimization of smoothened receptor. Med. Chem. Commun. 2017,8, 1332-1336.[Membrane Protein]

20.Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space.

Zhou, Q.; Sun, X.; Xia, X.; Fan, Z.; Luo, Z.; Zhao, S.; Shakhnovich, E.*; Liang, H.*, Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space. J Phys Chem Lett. 2017 Jan 19;8(2):407-414.

2016

19.Crystal Structure of the Human Cannabinoid Receptor CB1.

Hua, T.; Vemuri, K.; Pu, M.; Qu, L.; Han, G. W.; Wu, Y.; Zhao, S.; Shui, W.; Li, S.; Korde, A.; Laprairie, R. B.; Stahl, E. L.; Ho, J. H.; Zvonok, N.; Zhou, H.; Kufareva, I.; Wu, B.; Zhao, Q.; Hanson, M. A.; Bohn, L. M.*; Makriyannis, A.*; Stevens, R. C.*; Liu, Z. J.*, Crystal Structure of the Human Cannabinoid Receptor CB1. Cell. 2016 Oct 20;167(3):750-762.[Membrane Protein]

18.Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.

Zhang, X. S.; Carter, M. S.; Vetting, M. W.; Francisco, B. S.; Zhao, S.; Al-Obaidi, N. F.; Solbiati, J. O.; Thiaville, J. J.; de Crecy-Lagard, V.; Jacobson, M. P.; Almo, S. C.; Gerlt, J. A.*, Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161-9.[Pathway Docking and Genome Mining]

2015

17.Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Vetting, M. W.; Al-Obaidi, N.; Zhao, S.; San Francisco, B.; Kim, J.; Wichelecki, D. J.; Bouvier, J. T.; Solbiati, J. O.; Vu, H.; Zhang, X.; Rodionov, D. A.; Love, J. D.; Hillerich, B. S.; Seidel, R. D.; Quinn, R. J.*; Osterman, A. L.*; Cronan, J. E.*; Jacobson, M. P.*; Gerlt, J. A.*; Almo, S. C.*, Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry. 2015 Jan 27;54(3):909-31.[Pathway Docking and Genome Mining]

16.A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.

Zhang, X.; Kumar, R.; Vetting, M. W.; Zhao, S.; Jacobson, M. P.; Almo, S. C.; Gerlt, J. A.*, A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily. J Am Chem Soc. 2015 Feb 4;137(4):1388-91.[Pathway Docking and Genome Mining]

2014

15.Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.

Jacobson, M. P.*; Kalyanaraman, C.; Zhao, S.; Tian, B., Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci. 2014 Aug;39(8):363-71.[Pathway Docking and Genome Mining]

14.Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Zhao, S.; Sakai, A.; Zhang, X.; Vetting, M. W.; Kumar, R.; Hillerich, B.; San Francisco, B.; Solbiati, J.; Steves, A.; Brown, S.; Akiva, E.; Barber, A.; Seidel, R. D.; Babbitt, P. C.; Almo, S. C.*; Gerlt, J. A.*; Jacobson, M. P.*, Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3.[Pathway Docking and Genome Mining]

13.Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Kumar, R.;Zhao, S.; Vetting, M. W.; Wood, B. M.; Sakai, A.; Cho, K.; Solbiati, J.; Almo, S. C.; Sweedler, J. V.; Jacobson, M. P.; Gerlt, J. A.*; Cronan, J. E.*, Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio. 2014 Feb 11;5(1):e00933-13.[Pathway Docking and Genome Mining]

2013

12.Discovery of new enzymes and metabolic pathways by using structure and genome context.

Zhao, S.; Kumar, R.; Sakai, A.; Vetting, M. W.; Wood, B. M.; Brown, S.; Bonanno, J. B.; Hillerich, B. S.; Seidel, R. D.; Babbitt, P. C.; Almo, S. C.; Sweedler, J. V.*; Gerlt, J. A.*; Cronan, J. E.*; Jacobson, M. P.*, Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Oct 31;502(7473):698-702.[Pathway Docking and Genome Mining]

11.Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.

Tian, B.; Wallrapp, F.; Kalyanaraman, C.; Zhao, S.; Eriksson, L. A.*; Jacobson, M. P.*, Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase. Biochemistry. 2013 Aug 20;52(33):5511-3.

10.Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program.

Miller, E. B.; Murrett, C. S.; Zhu, K.; Zhao, S.; Goldfeld, D. A.; Bylund, J. H.; Friesner, R. A.*, Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program. J Chem Theory Comput. 2013 Mar 12;9(3):1846-4864.

2011

9.The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling.

Li, J.; Abel, R.; Zhu, K.; Cao, Y.; Zhao, S.; Friesner, R. A.*, The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 2011 Oct;79(10):2794-812.

8.Progress in super long loop prediction.

Zhao, S.; Zhu, K.; Li, J.; Friesner, R. A.*, Progress in super long loop prediction. Proteins. 2011 Oct;79(10):2920-35.

2008

7.Toward better refinement of comparative models: predicting loops in inexact environments.

Sellers, B. D.; Zhu, K.; Zhao, S.; Friesner, R. A.*; Jacobson, M. P.*, Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71.

2007

6.Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.

Li, X.; Jacobson, M. P.; Zhu, K.; Zhao, S.; Friesner, R. A.*, Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 2007 Mar 1;66(4):824-37.

2006

5.Long loop prediction using the protein local optimization program.

Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A.*, Long loop prediction using the protein local optimization program. Proteins. 2006 Nov 1;65(2):438-52.

2005

4.Assessment of the metabolic stability of the methyl groups in heterocyclic compounds using C-H bond dissociation energies: Effects of diverse aromatic groups on the stability of methyl radicals.

Zhao, S.; Liu, L.*; Fu, Y.; Guo, Q.X.*, Assessment of the metabolic stability of the methyl groups in heterocyclic compounds using C-H bond dissociation energies: Effects of diverse aromatic groups on the stability of methyl radicals. J Phys Org Chem. 2005, 18 (4), 353-367.

2004

3.Blue-shifted dihydrogen bonds.

Feng, Y.; Zhao, S.; Liu, L.*; Wang, J. T.; Li, X. S.; Guo, Q. X., Blue-shifted dihydrogen bonds. J Phys Org Chem. 2004, 17 (12), 1099-1106.

2.Origin of conformational restriction in complexes of formyl compounds with boron lewis acids and their related systems.

Feng, Y.; Liu, L.; Zhao, S.; Wang, J. T.; Guo, Q. X.*, Origin of conformational restriction in complexes of formyl compounds with boron lewis acids and their related systems. J. Phys. Chem. A. 2004, 108 (42), pp 9196–9204.

1.Homolytic C-H and N-H bond dissociation energies of strained organic compounds.

Feng, Y.; Liu, L.*; Wang, J. T.; Zhao, S.; Guo, Q. X.*, Homolytic C-H and N-H bond dissociation energies of strained organic compounds. J Org Chem. 2004 Apr 30;69(9):3129-38.