Academic Appointments

Honors & Awards

  • NIH Director's New Innovator Award, NIH (2015)
  • Klingenstein-Simons Fellow, The Klingenstein Fund and the Simons Foundation (2015)
  • Alfred P. Sloan Research Fellow, Alfred P. Sloan Foundation (2014)

Professional Education

  • PhD, Princeton University (2006)
  • MPhil, HKUST (2002)
  • B.S., Tsinghua University (1999)

Current Research and Scholarly Interests

Biological membranes act as selective barriers that separate the interior of cells from their outside environment. Membrane proteins play crucial roles in a wide range of biological and physiological processes and are targeted by a large number of pharmacologically active compounds including ~ 50% of the drugs in use today. Lack of high-resolution structural information has become a bottleneck for the mechanistic understanding of membrane proteins and hinders potential drug development. Our research interest lies primarily in understanding the mechanism and regulation of these dynamic membrane proteins, and developing small molecule modulators based on their structures and functions. We are taking a multi-disciplinary approach, employing structural methods to capture the high-resolution picture of different states, functional assays and biophysical methods to dissect the information inferred from the structure and computational approaches to understand their dynamics and kinetics.

2023-24 Courses

Stanford Advisees

All Publications

  • Structure and mechanism of the SGLT family of glucose transporters Nature Han, L., Qu, Q., Aydin, D., Panova, O., Robertson, M. J., Xu, Y., Dror, R. O., Skiniotis, G., Feng, L. 2022; 601: 274-279
  • Structure and mechanism of blood-brain-barrier lipid transporter MFSD2A. Nature Wood, C. A., Zhang, J., Aydin, D., Xu, Y., Andreone, B. J., Langen, U. H., Dror, R. O., Gu, C., Feng, L. 2021


    MFSD2A is a sodium-dependent lysophosphatidylcholine symporter that is responsible for the uptake of docosahexaenoic acid into the brain1,2, which is crucial for the development and performance of the brain3. Mutations that affect MFSD2A cause microcephaly syndromes4,5. The ability of MFSD2A to transport lipid is also a key mechanism that underlies its function as an inhibitor of transcytosis to regulate the blood-brain barrier6,7. Thus, MFSD2A represents an attractive target for modulating the permeability of the blood-brain barrier for drug delivery. Here we report the cryo-electron microscopy structure of mouse MFSD2A. Our structure defines the architecture of this important transporter, reveals its unique extracellular domain and uncovers its substrate-binding cavity. The structure-together with our functional studies and molecular dynamics simulations-identifies a conserved sodium-binding site, reveals a potential lipid entry pathway and helps to rationalize MFSD2A mutations that underlie microcephaly syndromes. These results shed light on the critical lipid transport function of MFSD2A and provide a framework to aid in the design of specific modulators for therapeutic purposes.

    View details for DOI 10.1038/s41586-021-03782-y

    View details for PubMedID 34349262

  • Structure and mechanism of the mitochondrial Ca2+ uniporter holocomplex. Nature Fan, M., Zhang, J., Tsai, C. W., Orlando, B. J., Rodriguez, M., Xu, Y., Liao, M., Tsai, M. F., Feng, L. 2020; 582 (7810): 129-133


    Mitochondria take up Ca2+ through the mitochondrial calcium uniporter complex to regulate energy production, cytosolic Ca2+ signalling and cell death1,2. In mammals, the uniporter complex (uniplex) contains four core components: the pore-forming MCU protein, the gatekeepers MICU1 and MICU2, and an auxiliary subunit, EMRE, essential for Ca2+ transport3-8. To prevent detrimental Ca2+ overload, the activity of MCU must be tightly regulated by MICUs, which sense changes in cytosolic Ca2+ concentrations to switch MCU on and off9,10. Here we report cryo-electron microscopic structures of the human mitochondrial calcium uniporter holocomplex in inhibited and Ca2+-activated states. These structures define the architecture of this multicomponent Ca2+-uptake machinery and reveal the gating mechanism by which MICUs control uniporter activity. Our work provides a framework for understanding regulated Ca2+ uptake in mitochondria, and could suggest ways of modulating uniporter activity to treat diseases related to mitochondrial Ca2+ overload.

    View details for DOI 10.1038/s41586-020-2309-6

    View details for PubMedID 32494073

  • Structure and mechanism of the cation-chloride cotransporter NKCC1. Nature Chew, T. A., Orlando, B. J., Zhang, J., Latorraca, N. R., Wang, A., Hollingsworth, S. A., Chen, D., Dror, R. O., Liao, M., Feng, L. 2019


    Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ion absorption and secretion across epithelia, and maintaining intracellular chloride homeostasis. These transporters are primary targets for some of the most commonly prescribed drugs. Here we determined the cryo-electron microscopy structure of the Na-K-Cl cotransporter NKCC1, an extensively studied member of the CCC family,from Danio rerio. The structure defines the architecture of this protein family and reveals how cytosolic and transmembrane domains are strategically positioned for communication. Structural analyses, functional characterizations and computational studies reveal the ion-translocation pathway, ion-binding sites and key residues for transport activity. These results provide insights into ion selectivity, coupling and translocation, and establish a framework for understanding the physiological functions of CCCs and interpreting disease-related mutations.

    View details for DOI 10.1038/s41586-019-1438-2

    View details for PubMedID 31367042

  • X-ray and cryo-EM structures of the mitochondrial calcium uniporter Nature Fan, C., Fan, M., Orlando, B., Fastman, N., Zhang, J., Xu, Y., Chambers, M., Xu, X., Perry, K., Liao, M., Feng, L. 2018
  • Mechanism of Substrate Translocation in an Alternating Access Transporter CELL Latorraca, N. R., Fastman, N. M., Venkatakrishnan, A. J., Frommer, W. B., Dror, R. O., Feng, L. 2017; 169 (1): 96-?


    Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations. Strikingly, these conformations match crystal structures, including our inward-open structure. Mutagenesis experiments further validate simulation predictions. Our results reveal that state transitions are driven by favorable interactions formed upon closure of extracellular and intracellular "gates" and by an unfavorable transmembrane helix configuration when both gates are closed. This mechanism leads to tight allosteric coupling between gates, preventing them from opening simultaneously. Interestingly, the substrate appears to take a "free ride" across the membrane without causing major structural rearrangements in the transporter.

    View details for DOI 10.1016/j.cell.2017.03.010

    View details for Web of Science ID 000397090000011

    View details for PubMedID 28340354

  • Structure of a eukaryotic SWEET transporter in a homotrimeric complex Nature Tao, Y., Cheung, L., Li, S., Eom, J., Chen, L., Xu, Y., Perry, K., Frommer, W., Feng, L. 2015

    View details for DOI 10.1038/nature15391

  • Structures of bacterial homologues of SWEET transporters in two distinct conformations NATURE Xu, Y., Tao, Y., Cheung, L. S., Fan, C., Chen, L., Xu, S., Perry, K., Frommer, W. B., Feng, L. 2014; 515 (7527): 448-?
  • Structure of a Eukaryotic CLC Transporter Defines an Intermediate State in the Transport Cycle SCIENCE Feng, L., Campbell, E. B., Hsiung, Y., MacKinnon, R. 2010; 330 (6004): 635-641


    CLC proteins transport chloride (Cl(-)) ions across cell membranes to control the electrical potential of muscle cells, transfer electrolytes across epithelia, and control the pH and electrolyte composition of intracellular organelles. Some members of this protein family are Cl(-) ion channels, whereas others are secondary active transporters that exchange Cl(-) ions and protons (H(+)) with a 2:1 stoichiometry. We have determined the structure of a eukaryotic CLC transporter at 3.5 angstrom resolution. Cytoplasmic cystathionine beta-synthase (CBS) domains are strategically positioned to regulate the ion-transport pathway, and many disease-causing mutations in human CLCs reside on the CBS-transmembrane interface. Comparison with prokaryotic CLC shows that a gating glutamate residue changes conformation and suggests a basis for 2:1 Cl(-)/H(+) exchange and a simple mechanistic connection between CLC channels and transporters.

    View details for DOI 10.1126/science.1195230

    View details for Web of Science ID 000283580600038

    View details for PubMedID 20929736

  • Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms NATURE Xu, Y., Feng, L., Jeffrey, P. D., Shi, Y., Morel, F. M. 2008; 452 (7183): 56-U3


    Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms, catalyses the reversible hydration of carbon dioxide and is used for inorganic carbon acquisition by phytoplankton. In the oceans, where zinc is nearly depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of sequence homology, CDCA is a structural mimic of a functional beta-carbonic anhydrase dimer, with striking similarity in the spatial organization of the active site residues. CDCA readily exchanges cadmium and zinc at its active site--an apparently unique adaptation to oceanic life that is explained by a stable opening of the metal coordinating site in the absence of metal. Given the central role of diatoms in exporting carbon to the deep sea, their use of cadmium in an enzyme critical for carbon acquisition establishes a remarkable link between the global cycles of cadmium and carbon.

    View details for DOI 10.1038/nature06636

    View details for Web of Science ID 000253671900045

    View details for PubMedID 18322527

  • Structure of a site-2 protease family intramembrane metalloprotease SCIENCE Feng, L., Yan, H., Wu, Z., Yan, N., Wang, Z., Jeffrey, P. D., Shi, Y. 2007; 318 (5856): 1608-1612


    Regulated intramembrane proteolysis by members of the site-2 protease (S2P) family is an important signaling mechanism conserved from bacteria to humans. Here we report the crystal structure of the transmembrane core domain of an S2P metalloprotease from Methanocaldococcus jannaschii. The protease consists of six transmembrane segments, with the catalytic zinc atom coordinated by two histidine residues and one aspartate residue approximately 14 angstroms into the lipid membrane surface. The protease exhibits two distinct conformations in the crystals. In the closed conformation, the active site is surrounded by transmembrane helices and is impermeable to substrate peptide; water molecules gain access to zinc through a polar, central channel that opens to the cytosolic side. In the open conformation, transmembrane helices alpha1 and alpha6 separate from each other by 10 to 12 angstroms, exposing the active site to substrate entry. The structure reveals how zinc embedded in an integral membrane protein can catalyze peptide cleavage.

    View details for DOI 10.1126/science.1150755

    View details for Web of Science ID 000251421700041

    View details for PubMedID 18063795

  • Structure of oxidized alpha-haemoglobin bound to AHSP reveals a protective mechanism for haem NATURE Feng, L., Zhou, S. P., Gu, L. C., Gell, D. A., MacKay, J. P., Weiss, M. J., Gow, A. J., Shi, Y. G. 2005; 435 (7042): 697-701


    The synthesis of haemoglobin A (HbA) is exquisitely coordinated during erythrocyte development to prevent damaging effects from individual alpha- and beta-subunits. The alpha-haemoglobin-stabilizing protein (AHSP) binds alpha-haemoglobin (alphaHb), inhibits the ability of alphaHb to generate reactive oxygen species and prevents its precipitation on exposure to oxidant stress. The structure of AHSP bound to ferrous alphaHb is thought to represent a transitional complex through which alphaHb is converted to a non-reactive, hexacoordinate ferric form. Here we report the crystal structure of this ferric alphaHb-AHSP complex at 2.4 A resolution. Our findings reveal a striking bis-histidyl configuration in which both the proximal and the distal histidines coordinate the haem iron atom. To attain this unusual conformation, segments of alphaHb undergo drastic structural rearrangements, including the repositioning of several alpha-helices. Moreover, conversion to the ferric bis-histidine configuration strongly and specifically inhibits redox chemistry catalysis and haem loss from alphaHb. The observed structural changes, which impair the chemical reactivity of haem iron, explain how AHSP stabilizes alphaHb and prevents its damaging effects in cells.

    View details for DOI 10.1038/nature03609

    View details for Web of Science ID 000229476200055

    View details for PubMedID 15931225

  • Molecular mechanism of AHSP-mediated stabilization of alpha-hemoglobin CELL Feng, L., Gell, D. A., Zhou, S. P., Gu, L. C., Kong, Y., Li, J. Q., Hu, M., Yan, N., Lee, C., Rich, A. M., Armstrong, R. S., Lay, P. A., Gow, A. J., Weiss, M. J., Mackay, J. P., Shi, Y. G. 2004; 119 (5): 629-640


    Hemoglobin A (HbA), the oxygen delivery system in humans, comprises two alpha and two beta subunits. Free alpha-hemoglobin (alphaHb) is unstable, and its precipitation contributes to the pathophysiology of beta thalassemia. In erythrocytes, the alpha-hemoglobin stabilizing protein (AHSP) binds alphaHb and inhibits its precipitation. The crystal structure of AHSP bound to Fe(II)-alphaHb reveals that AHSP specifically recognizes the G and H helices of alphaHb through a hydrophobic interface that largely recapitulates the alpha1-beta1 interface of hemoglobin. The AHSP-alphaHb interactions are extensive but suboptimal, explaining why beta-hemoglobin can competitively displace AHSP to form HbA. Remarkably, the Fe(II)-heme group in AHSP bound alphaHb is coordinated by the distal but not the proximal histidine. Importantly, binding to AHSP facilitates the conversion of oxy-alphaHb to a deoxygenated, oxidized [Fe(III)], nonreactive form in which all six coordinate positions are occupied. These observations reveal the molecular mechanisms by which AHSP stabilizes free alphaHb.

    View details for Web of Science ID 000225389500009

    View details for PubMedID 15550245

  • Structure and function of SemiSWEET and SWEET sugar transporters TRENDS IN BIOCHEMICAL SCIENCES Feng, L., Frommer, W. B. 2015; 40 (8): 480-486


    SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure-function relations in this new class of transporters.

    View details for DOI 10.1016/j.tibs.2015.05.005

    View details for Web of Science ID 000358805800008

  • Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Feng, L., Campbell, E. B., MacKinnon, R. 2012; 109 (29): 11699-11704


    CLC proteins underlie muscle, kidney, bone, and other organ system function by catalyzing the transport of Cl(-) ions across cell and organellar membranes. Some CLC proteins are ion channels while others are pumps that exchange Cl(-) for H(+). The pathway through which Cl(-) ions cross the membrane has been characterized, but the transport of H(+) and the principle by which their movement is coupled to Cl(-) movement is not well understood. Here we show that H(+) transport depends not only on the presence of a specific glutamate residue but also the presence of Cl(-) ions. H(+) transport, however, can be isolated and analyzed in the absence of Cl(-) by mutating the glutamate to alanine and adding carboxylate-containing molecules to solution, consistent with the notion that H(+) transfer is mediated through the entry of a carboxylate group into the anion pathway. Cl(-) ions and carboxylate interact with each other strongly. These data support a mechanism in which the glutamate carboxylate functions as a surrogate Cl(-) ion, but it can accept a H(+) and transfer it between the external solution and the central Cl(-) binding site, coupled to the movement of 2 Cl(-) ions.

    View details for DOI 10.1073/pnas.1205764109

    View details for Web of Science ID 000306837100047

    View details for PubMedID 22753511

  • A cis-Proline in alpha-Hemoglobin Stabilizing Protein Directs the Structural Reorganization of alpha-Hemoglobin JOURNAL OF BIOLOGICAL CHEMISTRY Gell, D. A., Feng, L., Zhou, S., Jeffrey, P. D., Bendak, K., Gow, A., Weiss, M. J., Shi, Y., Mackay, J. P. 2009; 284 (43): 29462-29469


    alpha-Hemoglobin (alphaHb) stabilizing protein (AHSP) is expressed in erythropoietic tissues as an accessory factor in hemoglobin synthesis. AHSP forms a specific complex with alphaHb and suppresses the heme-catalyzed evolution of reactive oxygen species by converting alphaHb to a conformation in which the heme is coordinated at both axial positions by histidine side chains (bis-histidyl coordination). Currently, the detailed mechanism by which AHSP induces structural changes in alphaHb has not been determined. Here, we present x-ray crystallography, NMR spectroscopy, and mutagenesis data that identify, for the first time, the importance of an evolutionarily conserved proline, Pro(30), in loop 1 of AHSP. Mutation of Pro(30) to a variety of residue types results in reduced ability to convert alphaHb. In complex with alphaHb, AHSP Pro(30) adopts a cis-peptidyl conformation and makes contact with the N terminus of helix G in alphaHb. Mutations that stabilize the cis-peptidyl conformation of free AHSP, also enhance the alphaHb conversion activity. These findings suggest that AHSP loop 1 can transmit structural changes to the heme pocket of alphaHb, and, more generally, highlight the importance of cis-peptidyl prolyl residues in defining the conformation of regulatory protein loops.

    View details for DOI 10.1074/jbc.M109.027045

    View details for Web of Science ID 000270896800028

    View details for PubMedID 19706593

  • Enzymatic analysis of a rhomboid intramembrane protease implicates transmembrane helix 5 as the lateral substrate gate PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Baker, R. P., Young, K., Feng, L., Shi, Y., Urban, S. 2007; 104 (20): 8257-8262


    Intramembrane proteolysis is a core regulatory mechanism of cells that raises a biochemical paradox of how hydrolysis of peptide bonds is accomplished within the normally hydrophobic environment of the membrane. Recent high-resolution crystal structures have revealed that rhomboid proteases contain a catalytic serine recessed into the plane of the membrane, within a hydrophilic cavity that opens to the extracellular face, but protected laterally from membrane lipids by a ring of transmembrane segments. This architecture poses questions about how substrates enter the internal active site laterally from membrane lipid. Because structures are static glimpses of a dynamic enzyme, we have taken a structure-function approach analyzing >40 engineered variants to identify the gating mechanism used by rhomboid proteases. Importantly, our analyses were conducted with a substrate that we show is cleaved at two intramembrane sites within the previously defined Spitz substrate motif. Engineered mutants in the L1 loop and active-site region of the GlpG rhomboid protease suggest an important structural, rather than dynamic, gating function for the L1 loop that was first proposed to be the substrate gate. Conversely, three classes of mutations that promote transmembrane helix 5 displacement away from the protease core dramatically enhanced enzyme activity 4- to 10-fold. Our functional analyses have identified transmembrane helix 5 movement to gate lateral substrate entry as a rate-limiting step in intramembrane proteolysis. Moreover, our mutagenesis also underscores the importance of other residue interactions within the enzyme that warrant further scrutiny.

    View details for DOI 10.1073/pnas.0700814104

    View details for Web of Science ID 000246599900014

    View details for PubMedID 17463085

  • Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry NATURE STRUCTURAL & MOLECULAR BIOLOGY Wu, Z., Yan, N., Feng, L., Oberstein, A., Yan, H., Baker, R. P., Gu, L., Jeffrey, P. D., Urban, S., Shi, Y. 2006; 13 (12): 1084-1091


    Intramembrane proteolysis regulates diverse biological processes. Cleavage of substrate peptide bonds within the membrane bilayer is catalyzed by integral membrane proteases. Here we report the crystal structure of the transmembrane core domain of GlpG, a rhomboid-family intramembrane serine protease from Escherichia coli. The protein contains six transmembrane helices, with the catalytic Ser201 located at the N terminus of helix alpha4 approximately 10 A below the membrane surface. Access to water molecules is provided by a central cavity that opens to the extracellular region and converges on Ser201. One of the two GlpG molecules in the asymmetric unit has an open conformation at the active site, with the transmembrane helix alpha5 bent away from the rest of the molecule. Structural analysis suggests that substrate entry to the active site is probably gated by the movement of helix alpha5.

    View details for DOI 10.1038/nsmb1179

    View details for Web of Science ID 000242655600013

    View details for PubMedID 17099694

  • Simple bioseparations using self-cleaving elastin-like polypeptide tags NATURE METHODS Banki, M. R., Feng, L. A., Wood, D. W. 2005; 2 (9): 659-661


    We introduce a new method for the purification of recombinant proteins expressed in Escherichia coli using self-cleaving elastin-like polypeptide (ELP) fusion tags without the need for affinity chromatography or proteolytic tag removal. Using this method we obtained high purity, activity and reasonable yields for ten diverse target proteins.

    View details for Web of Science ID 000235261900017

    View details for PubMedID 16074986

  • A repetitive element containing a critical tyrosine residue is required for transcriptional activation by the EWS/ATF1 oncogene ONCOGENE Feng, L., Lee, K. A. 2001; 20 (31): 4161-4168


    Chromosomal fusion of the N-terminal region of the Ewings Sarcoma Oncogene (EWS-activation-domain, EAD) to the DNA-binding domains of a variety of cellular transcription factors produce oncogenic proteins (EWS-fusion proteins (EFPs)) that cause distinct malignancies. In EFPs, the EAD acts as a potent transcriptional activation domain and this ability is repressed in the context of normal, non-tumorigenic, EWS. Trans-activation by the EAD is therefore a specific characteristic of EFPs and it is thought that EFPs induce tumorigenesis via improper transcriptional activation of cellular genes. Functional elements required for transcriptional activation are dispersed throughout the EAD, as are thirty-one copies of a Degenerate Hexapeptide Repeat (DHR, consensus SYGQQS). This suggests that the EAD contains a highly reiterated functional element related to DHRs. Here we show that in the context of EWS/ATF1, the EFP that causes malignant melanoma of soft parts, trans-cooperation by small regions of the EAD ( approximately 30 residues) results in potent transcriptional activation dependent on the conserved tyrosine residues present in DHRs. These findings provide the first evidence for a role of DHRs in EAD-mediated trans-activation and demonstrate that the EAD represents a novel tyrosine-dependent transcriptional activation domain.

    View details for Web of Science ID 000169857200006

    View details for PubMedID 11464282