Weill Medical College  of Cornell University
Weill Medical College  of Cornell University Cornell University
Department of Physiology and Biophysics
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Lei Shi

Publications:

Journal articles (#denotes equal contribution, *denotes corresponding authorship)

#Zhao C, #Stolzenberg S, Gracia L, Weinstein H, Noskov S*, Shi L*. Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT. Biophys J. in press

*Newman AH, Beuming T, Banala A, Donthamsetti P, Pongetti K, Labounty A, Levy B, Cao J, Michino M, Luedtke R, *Javitch JA, *Shi L. Molecular Determinants of Selectivity and Efficacy at the Dopamine D3 Receptor. J Med Chem. 2012 Aug 9;55(15):6689-99. Epub 2012 Jun 7. [pubmed] [comment in] [cover]

Loland CJ, Mereu M, Okunola O, Cao J, Prisinzano TE, Mazier S, Kopajtic T, Shi L, Katz JL, Tanda G, Newman AH*. R-modafinil (armodafinil): a unique dopamine uptake inhibitor and potential medication for psychostimulant abuse. Biological Psychiatry. 2012 Sep 1;72(5):405-13. Epub 2012 Apr 25. [pubmed] [comment in] [cover]

Quick M, Shi L, Zehnpfennig B, Weinstein H, *Javitch JA. Experimental conditions can obscure the second high-affinity site in LeuT. Nat Struct Mol Biol. 2012 Jan 15;19(2):207-11. [pubmed] [comment in]

Mazier S, *Quick M, *Shi L. A conserved Tyr in the first transmembrane segment of Solute:Sodium Symporters is involved in Na+-coupled substrate co-transport. J Biol Chem. 2011 Jun 24. [pubmed] [scholar]

#Zhao Y, #Terry D, #Shi L, Quick M,*Weinstein H, *Blanchard SC, *Javitch JA. Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homolog.Nature. 2011 Apr 24. [pubmed] [scholar] [press release]

Shan J, Javitch JA, *Shi L, *Weinstein H. The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter.PLoS One. 2011 Jan 27;6(1):e16350. [pubmed] [scholar]

*Shi L, *Weinstein H, Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms.Biophys J. 2010 Dec 15;99(12):L103-5. [ [pubmed] [scholar]

Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, *Stevens RC. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.Science. 2010 Nov 19;330(6007):1091-5. [ [pubmed] [scholar] [in the news]

Bisgaard H, Larsen MA, Mazier S, Beuming T, Newman AH, Weinstein H, *Shi L, *Loland CJ, *Gether U. The binding sites for benztropines and dopamine in the dopamine transporter overlap.Neuropharmacology. 2011 Jan;60(1):182-90. Epub 2010 Sep 6. [ [pubmed] [scholar]

Claxton DP, Quick M, Shi L, de Carvalho FD, Weinstein H, Javitch JA, *Mchaourab HS. Ion/substrate-dependent conformational dynamics of a bacterial transporter homolog of neurotransmitter:sodium symporters.Nat Struct Mol Biol. 2010 Jul;17(7):822-9. Epub 2010 Jun 20. [pubmed] [scholar]

*Shi L, Srdanovic M, Beuming T, Skrabanek L, Javitch JA, *Weinstein H. TRAC — a platform for structure-function studies of NSS-proteins integrates information from bioinformatics and biomedical literature. Bioinformatics and BioEngineering, 2010. BIBE '10. Tenth IEEE International Conference on. 2010.[ieeexplore] [ieeecomputersociety]

#Zhao Y, #Terry D, Shi L, Weinstein H, Blanchard SC, *Javitch JA. Single-molecule dynamics of gating in a neurotransmitter transporter homolog. Nature. 2010 May 13;465(7295):188-93 [pubmed] [scholar] [comment] [press release]

#Zhao Y, #Quick M, Shi L, Mehler EL, Weinstein H, *Javitch JA. Substrate-dependent proton antiport in neurotransmitter:sodium symporters. Nat Chem Biol. 2010 Feb;6(2):109-16. Epub 2009 Dec 27. [pubmed] [scholar]

#Quick M, #Winther AL, #Shi L, Nissen P, Weinstein H, *Javitch JA. Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5563-8. Epub 2009 Mar 23. [pubmed] [scholar]

Guptaroy B, Zhang M, Bowton E, Binda F, Shi L, Weinstein H, Galli A, Javitch JA, Neubig RR, *Gnegy ME. A juxtamembrane mutation in the n-terminus of the dopamine transporter induces preference for an inward-facing conformation. Mol Pharmacol. 2009 Jan 5. [pubmed] [scholar]

Guo W, Urizar E, Kralikova M, Mobarec JC, Shi L, Filizola M, *Javitch JA. Dopamine D2 receptors form higher order oligomers at physiological expression levels. EMBO J. 2008 Sep 3;27(17):2293-304. [pubmed] [scholar]

Wang D, Yang H, Shi L, Ma L, Fujii T, Engelstad K, Pascual JM, *De Vivo DC. Functional studies of the T295M mutation Causing Glut1 Deficiency: Glucose efflux preferentially affected by T295M. Pediatr Res. 2008 Nov;64(5):538-43. [pubmed] [scholar]

#Shi L, #Quick M, Zhao Y, Weinstein H, and *Javitch JA The mechanism of a neurotransmitter:sodium symporter—inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell. 2008 Jun 20;30(6):667-77. [pubmed] [cover] [press release]

Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, *Gether U, and Loland CJ. The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci. 2008 Jul;11(7):780-9. Epub 2008 Jun 22. [pubmed] [scholar] [press release]

#Kniazeff J, #Shi L, Loland CJ, Javitch JA, *Weinstein H, *Gether U. An intracellular interaction network regulates conformational transitions in the dopamine transporter. J Biol Chem. 2008 Jun 20;283(25):17691-701. Epub 2008 Apr 21. [pubmed] [scholar]

Pascual JM, Wang D, Yang R, Shi L, Yang H, *De Vivo DC. Structural signatures and membrane helix 4 in GLUT1: Inferences from human blood brain glucose transport mutants. J Biol Chem. 2008 Jun 13;283(24):16732-42. Epub 2008 Apr 3. [pubmed] [scholar]

#Beuming T, #Shi L, *Javitch JA, and *Weinstein H. A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol. 2006 Nov;70(5):1630-42. Epub 2006 Jul 31. [pubmed] [scholar] [TRAC]

Quick M, Yano H, Goldberg NR, Duan L, Beuming T, Shi L, Weinstein H, and *Javitch JA. State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter: sodium symporter from Fusobacterium nucleatum. J Biol Chem. 2006, Jun 23. [pubmed] [scholar]

*Shi L and *Javitch JA. Information collection, management, and integration in structure-function studies of G-protein coupled receptors. Curr Pharm Des. 2006, 12(14):1771-83. [pubmed] [scholar]

Hao G, Derakhshan B, Shi L, Campagne F, and *Gross SS. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc. Natl. Acad. Sci. USA 2006, 103(4):1012-7. [pubmed] [scholar] [press release]

Guo W, #Shi L, #Filizola M, Weinstein H, *Javitch JA. A structural context for functional crosstalk in G-protein-coupled receptors: dynamic changes at the homodimer interface in the transmembrane domain determine activation. Proc. Natl. Acad. Sci. USA 2005, 102(48):17495-500. [pubmed] [scholar] [press release] [“from the cover”] [jpet cover]

Sen N, Shi L, Beuming T, Weinstein H, and *Javitch JA. A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding. Neuropharmacology 2005, 49(6):780-90. [pubmed] [scholar]

Carter M, Chen X, Minnerath S, Slowinska B, Shi L, Champagne F, Weinstein H, and *Ross ME. Crooked tail (Cd) model of human folate responsive NTD is mutated in Wnt co-receptor, Lrp6. Proc. Natl. Acad. Sci. USA 2005, 102(36):12843-8. [pubmed] [scholar]

Palma M, Zurita J, Ferreras J, Worgall S, Larone DH, Shi L, Campagne F, and *Quadri LE. Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infection and Immunity 2005, 73(5):2958-66.  [pubmed] [scholar]

Shi L and *Campagne F. Building a protein name dictionary from full text: a machine learning term extraction approach. BMC bioinformatics 2005, 6(1):88. [pubmed] [scholar]

Shi L and *Javitch JA. The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice. Proc. Natl. Acad. Sci. USA 2004, 101(1):440-5. [pubmed] [scholar]

Yu Y, Shi L, and *Karlin A. Structural effects of quinacrine binding in the open channel of the acetylcholine receptor. Proc. Natl. Acad. Sci. USA 2003, 100(7):3907-12. [pubmed] [scholar]

Li J, Shi L, and *Karlin A. A photochemical approach to the lipid accessibility of engineered cysteinyl residues. Proc. Natl. Acad. Sci. USA 2003, 100(3):886-91. [pubmed] [scholar]

Guo W, Shi L, and *Javitch JA. The fourth transmembrane segment forms the dopamine D2 receptor homodimer interface. J. Biol. Chem. 2003, 278(7):4385-8. [pubmed] [press release] [scholar]

#Shi L, #Liapakis G, Xu R, Guarnieri F, Ballesteros JA, and *Javitch JA. β2 Adrenergic Receptor Activation: Modulation of the Proline Kink in TM6 by a Rotamer Toggle Switch. J. Biol. Chem. 2002, 277(43):40989-96. [pubmed] [scholar]

Shi L and *Javitch JA. The binding site of aminergic G-protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu. Rev. Pharmacol. Toxicol. 2002, 42:437-67. [pubmed] [scholar]

*Javitch JA, Shi L, and Liapakis G. Use of the substituted-cysteine accessibility method (SCAM) to study the structure and function of G-protein-coupled receptors. Methods Enzymol. 2002, 343:137-56. [pubmed] [scholar]

Shi L, Simpson MM, Ballesteros JA, and *Javitch JA. The first transmembrane segment of the dopamine D2 receptor: accessibility in the binding-site crevice and position in the transmembrane bundle. Biochemistry 2001, 40(41): 12339-48. [pubmed] [scholar]

Xu W, Li J, Chen C, Huang P, Weinstein H, Javitch JA, Shi L, Riel JK, and *Liu-Chen L. Comparison of the amino acid residues in the sixth transmembrane domains accessible in binding-site crevices of m, d and k opioid receptors. Biochemistry 2001, 40(27):8018-29. [pubmed] [scholar]

#Ballesteros J A, #Shi L, and *Javitch JA. Structural mimicry in G-protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol. Pharmacol. 2001, 60(1):1-19.  [pubmed][scholar] [cover]

Ballesteros JA, Jensen AD, Liapakis G, Rasmussen SG, Shi L, Gether U, and *Jonathan A. Javitch, JA. Activation of the β2 adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6. J. Biol. Chem. 2001, 276(31):29171-7. [pubmed] [scholar]

*Javitch JA, Shi L, Simpson MM, Chen J, Chiappa V, Visiers I, Weinstein H, and Ballesteros JA. The fourth transmembrane segment of the dopamine D2 receptor: accessibility in the binding-site crevice and position in the transmembrane bundle. Biochemistry 2000, 39(40):12190-9. [pubmed] [scholar]

Saunders C, Ferrer JV, Shi L, Chen J, Merrill G, Lamb ME, Leeb-Lundberg LM, Carvelli L, Javitch JA, and *Galli A. Amphetamine-induced loss of human dopamine transporter activity: An internalization-dependent and cocaine-sensitive mechanism. Proc. Natl. Acad. Sci. USA 2000, 97(12): 6850-6855. [pubmed] [scholar]

Book chapters

Shi L. Molecular Modeling and Simulations of Transporter Proteins — the Transmembrane Allosteric Machinery. Comprehensive Biophysics, Elsevier, Amsterdam, Netherlands 2012. [DOI]

Moreira IS, Shi L, Freyberg Z, Eriksen SS, Weinstein H, Javitch JA. Structural Basis of Dopamine Receptor Activation. The Dopamine Receptors, 2nd Edition, Humana Press, Totowa, NJ 2009 [DOI]

Deupi X, Govaerts C, Shi L, Javitch J, Pardo L, and Ballesteros JA. Conformational plasticity of GPCR binding sites: structural basis for evolutionary diversity in ligand recognition. The G Protein-Coupled Receptors Handbook, Humana Press, Totowa, NJ 2005 [DOI]

Shi L and Javitch JA. The binding pocket of G protein-coupled receptors for biogenic amines, retinal, and other ligands. Handbook of Cell Signaling, Academic Press, San Diego, CA 2003 [DOI]

physiology@med.cornell.edu | last updated: Friday, September 30, 2005