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Professor Liz Carpenter

Research Area: Protein Science and Structural Biology
Technology Exchange: Crystallography, Drug discovery and Protein interaction
Scientific Themes: Protein Science & Structural Biology and Physiology, Cellular & Molecular Biology
Keywords: Membrane proteins, X-ray crystallography, Protein structure, ion channels, high throughput methods and drug design
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Membrane proteins are the gateways to the cell. All cells and organelles are surrounded by an oily, impermeable lipid bilayer and many small molecules can only cross this barrier by passing through protein molecules embedded in the bilayer. Many nutrients, ions, waste products and even DNA and proteins enter and leave cells only via proteins which are tightly controlled, thus maintaining the integrity of the cell. Communication between cells is also mediated by these proteins often by binding signaling molecules outside cells and amplifying the signal by triggering chemical reactions inside the cell. These diverse functions are fulfilled by a huge variety of membrane proteins, in fact approximately 15% of all the genes in the human genome code for these proteins. Given their location on the surfaces of cells, it is not surprising that membrane proteins are often found to be the targets for drugs, such as the calcium channel blockers used to treat heart disease and potassium channel blockers which are used in diabetes treatment. Indeed membrane proteins are involved in the development of many diseases, including heart disease, cancer, cystic fibrosis, Alzheimer’s, Parkinson’s and other neurological diseases, kidney disease and epilepsy.

My group at the structural Genomics Consortium in Oxford aims to solve the three dimensional structures of human membrane proteins using X-ray crystallography. We purify proteins, pursuad them to form crystals, and then expose them to a beam of X-rays. The resulting diffraction patterns can then be used to understand the positions of all the atoms in the protein. We then study the structures in complex with inhibitors and drugs, using this information to improve and extend the available treatments for disease. There are less than 50 structures of human membrane proteins known and we therefore seak to develop methods to make this process more efficient. In the past four years we have established a working high-throughput system for the producing human membrane proteins for structural studies.

The IMP group at the SGC studies proteins from a variety membrane protein families, including ion channels enzymes and ABC transporters. To date we have solved structures of of proteins in three different areas:

1. We solved the first structure of a human ABC transporter, ABCB10, a mitochondrial protein which is important for heme production and for resistance of mitochondria to oxidative stress.

2. Premature ageing syndromes can be caused by a failure in the processing of the lamin proteins, which form a network of fibres underlying the nuclear membrane within cells. We have solved the structure of a zinc metalloprotease, ZMPSTE24, which is responsible for two steps in this processing. This structure has allowed us to see how mutations in the ZMPSTE24 protein can lead to premature ageing diseases, which provide a model for normal ageing.

3. Recently we have solved and deposited the structure of a human ion channel, TREK-2, one of the family of K2P proteins which are responsible for the background leak current that helps to maintain the membrane potential and also are susceptible to a range of physiological and pharmacological stimuli.

Name Department Institution Country
Professor Juha T Huiskonen Structural Biology University of Oxford United Kingdom
Dr Nicola A Burgess-Brown Structural Genomics Consortium University of Oxford United Kingdom
Professor Wyatt W Yue Structural Genomics Consortium University of Oxford United Kingdom
Dr Brian D Marsden Structural Genomics Consortium University of Oxford United Kingdom
Professor Paul Brennan Target Discovery Institute University of Oxford United Kingdom
Dr Frank von Delft Structural Genomics Consortium University of Oxford United Kingdom
Prof David Beeson (RDM) Weatherall Institute of Molecular Medicine University of Oxford United Kingdom

McClenaghan C, Schewe M, Aryal P, Carpenter EP, Baukrowitz T, Tucker SJ. 2016. Polymodal activation of the TREK-2 K2P channel produces structurally distinct open states. J Gen Physiol, 147 (6), pp. 497-505. Read abstract | Read more

The TREK subfamily of two-pore domain (K2P) K(+) channels exhibit polymodal gating by a wide range of physical and chemical stimuli. Crystal structures now exist for these channels in two main states referred to as the "up" and "down" conformations. However, recent studies have resulted in contradictory and mutually exclusive conclusions about the functional (i.e., conductive) status of these two conformations. To address this problem, we have used the state-dependent TREK-2 inhibitor norfluoxetine that can only bind to the down state, thereby allowing us to distinguish between these two conformations when activated by different stimuli. Our results reconcile these previously contradictory gating models by demonstrating that activation by pressure, temperature, voltage, and pH produce more than one structurally distinct open state and reveal that channel activation does not simply involve switching between the up and down conformations. These results also highlight the diversity of structural mechanisms that K2P channels use to integrate polymodal gating signals. Hide abstract

Pike AC, Garman EF, Krojer T, von Delft F, Carpenter EP. 2016. An overview of heavy-atom derivatization of protein crystals. Acta Crystallogr D Struct Biol, 72 (Pt 3), pp. 303-318. Read abstract | Read more

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative. Hide abstract

Dong YY, Pike AC, Mackenzie A, McClenaghan C, Aryal P, Dong L, Quigley A, Grieben M et al. 2015. K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac. Science, 347 (6227), pp. 1256-1259. Read abstract | Read more

TREK-2 (KCNK10/K2P10), a two-pore domain potassium (K2P) channel, is gated by multiple stimuli such as stretch, fatty acids, and pH and by several drugs. However, the mechanisms that control channel gating are unclear. Here we present crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. These results provide an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac. Hide abstract

Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MS. 2015. MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure, 23 (7), pp. 1350-1361. Read abstract | Read more

There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein. Hide abstract

Qiu W, Liesa M, Carpenter EP, Shirihai OS. 2015. ATP Binding and Hydrolysis Properties of ABCB10 and Their Regulation by Glutathione. PLoS One, 10 (6), pp. e0129772. Read abstract | Read more

ABCB10 (ATP binding cassette sub-family B10) is a mitochondrial inner-membrane ABC transporter. ABCB10 has been shown to protect the heart from the impact of ROS during ischemia-reperfusion and to allow for proper hemoglobin synthesis during erythroid development. ABC transporters are proteins that increase ATP binding and hydrolysis activity in the presence of the transported substrate. However, molecular entities transported by ABCB10 and its regulatory mechanisms are currently unknown. Here we characterized ATP binding and hydrolysis properties of ABCB10 by using the 8-azido-ATP photolabeling technique. This technique can identify potential ABCB10 regulators, transported substrates and amino-acidic residues required for ATP binding and hydrolysis. We confirmed that Gly497 and Lys498 in the Walker A motif, Glu624 in the Walker B motif and Gly602 in the C-Loop motif of ABCB10 are required for proper ATP binding and hydrolysis activity, as their mutation changed ABCB10 8-Azido-ATP photo-labeling. In addition, we show that the potential ABCB10 transported entity and heme precursor delta-aminolevulinic acid (dALA) does not alter 8-azido-ATP photo-labeling. In contrast, oxidized glutathione (GSSG) stimulates ATP hydrolysis without affecting ATP binding, whereas reduced glutathione (GSH) inhibits ATP binding and hydrolysis. Indeed, we detectABCB10 glutathionylation in Cys547 and show that it is one of the exposed cysteine residues within ABCB10 structure. In all, we characterize essential residues for ABCB10 ATPase activity and we provide evidence that supports the exclusion of dALA as a potential substrate directly transported by ABCB10. Last, we show the first molecular mechanism by which mitochondrial oxidative status, through GSH/GSSG, can regulate ABCB10. Hide abstract

Deme JC, Hancock MA, Xia X, Shintre CA, Plesa M, Kim JC, Carpenter EP, Rosenblatt DS, Coulton JW. 2014. Purification and interaction analyses of two human lysosomal vitamin B12 transporters: LMBD1 and ABCD4. Mol Membr Biol, 31 (7-8), pp. 250-261. Read abstract | Read more

Mutations in human LMBRD1 and ABCD4 prevent lysosomal export of vitamin B(12) to the cytoplasm, impairing the vitamin B(12)-dependent enzymes methionine synthase and methylmalonyl-CoA mutase. The gene products of LMBRD1 and ABCD4 are implicated in vitamin B(12) transport at the lysosomal membrane and are proposed to act in complex. To address the mechanism for lysosomal vitamin B(12) transport, we report the novel recombinant production of LMBD1 and ABCD4 for detailed biophysical analyses. Using blue native PAGE, chemical crosslinking, and size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), we show that both detergent-solubilized LMBD1 and detergent-solubilized ABCD4 form homodimers. To examine the functional binding properties of these proteins, label-free surface plasmon resonance (SPR) provides direct in vitro evidence that: (i) LMBD1 and ABCD4 interact with low nanomolar affinity; and (ii) the cytoplasmic vitamin B(12)-processing protein MMACHC also interacts with LMBD1 and ABCD4 with low nanomolar affinity. Accordingly, we propose a model whereby membrane-bound LMBD1 and ABCD4 facilitate the vectorial delivery of lysosomal vitamin B(12) to cytoplasmic MMACHC, thus preventing cofactor dilution to the cytoplasmic milieu and protecting against inactivating side reactions. Hide abstract

Shintre CA, Pike AC, Li Q, Kim JI, Barr AJ, Goubin S, Shrestha L, Yang J et al. 2013. Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states. Proc Natl Acad Sci U S A, 110 (24), pp. 9710-9715. Read abstract | Read more

ABCB10 is one of the three ATP-binding cassette (ABC) transporters found in the inner membrane of mitochondria. In mammals ABCB10 is essential for erythropoiesis, and for protection of mitochondria against oxidative stress. ABCB10 is therefore a potential therapeutic target for diseases in which increased mitochondrial reactive oxygen species production and oxidative stress play a major role. The crystal structure of apo-ABCB10 shows a classic exporter fold ABC transporter structure, in an open-inwards conformation, ready to bind the substrate or nucleotide from the inner mitochondrial matrix or membrane. Unexpectedly, however, ABCB10 adopts an open-inwards conformation when complexed with nonhydrolysable ATP analogs, in contrast to other transporter structures which adopt an open-outwards conformation in complex with ATP. The three complexes of ABCB10/ATP analogs reported here showed varying degrees of opening of the transport substrate binding site, indicating that in this conformation there is some flexibility between the two halves of the protein. These structures suggest that the observed plasticity, together with a portal between two helices in the transmembrane region of ABCB10, assist transport substrate entry into the substrate binding cavity. These structures indicate that ABC transporters may exist in an open-inwards conformation when nucleotide is bound. We discuss ways in which this observation can be aligned with the current views on mechanisms of ABC transporters. Hide abstract

Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS et al. 2013. The structural basis of ZMPSTE24-dependent laminopathies. Science, 339 (6127), pp. 1604-1607. Read abstract | Read more

Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lamina intermediate filaments, by cleaving it at two sites. Failure of this processing results in accumulation of farnesylated, membrane-associated prelamin A. The 3.4 angstrom crystal structure of human ZMPSTE24 has a seven transmembrane α-helical barrel structure, surrounding a large, water-filled, intramembrane chamber, capped by a zinc metalloprotease domain with the catalytic site facing into the chamber. The 3.8 angstrom structure of a complex with a CSIM tetrapeptide showed that the mode of binding of the substrate resembles that of an insect metalloprotease inhibitor in thermolysin. Laminopathy-associated mutations predicted to reduce ZMPSTE24 activity map to the zinc metalloprotease peptide-binding site and to the bottom of the chamber. Hide abstract

Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS. 2012. Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc Natl Acad Sci U S A, 109 (42), pp. 16852-16857. Read abstract | Read more

Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures. Hide abstract

Bailey D, Carpenter EP, Coker A, Coker S, Read J, Jones AT, Erskine P, Aguilar CF et al. 2012. An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases. Acta Crystallogr D Biol Crystallogr, 68 (Pt 5), pp. 541-552. Read abstract | Read more

The analysis reported here describes detailed structural studies of endothiapepsin (the aspartic proteinase from Endothia parasitica), with and without bound inhibitors, and human pepsin 3b. Comparison of multiple crystal structures of members of the aspartic proteinase family has revealed small but significant differences in domain orientation in different crystal forms. In this paper, it is shown that these differences in domain orientation do not necessarily correlate with the presence or absence of bound inhibitors, but appear to stem at least partly from crystal contacts mediated by sulfate ions. However, since the same inherent flexibility of the structure is observed for other enzymes in this family such as human pepsin, the native structure of which is also reported here, the observed domain movements may well have implications for the mechanism of catalysis. Hide abstract

Berridge G, Chalk R, D'Avanzo N, Dong L, Doyle D, Kim JI, Xia X, Burgess-Brown N, Deriso A, Carpenter EP, Gileadi O. 2011. High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins Analytical Biochemistry, 410 (2), pp. 272-280. Read abstract | Read more

We have developed a method for intact mass analysis of detergent- solubilized and purified integral membrane proteins using liquid chromatography-mass spectrometry (LC-MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2-5 μg of protein. The method is also compatible with our standard LC-MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment. © 2010 Elsevier Inc. All rights reserved. Hide abstract

Newstead S, Drew D, Cameron AD, Postis VLG, Xia X, Fowler PW, Ingram JC, Carpenter EP et al. 2011. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2 EMBO Journal, 30 (2), pp. 417-426. Read abstract | Read more

PepT1 and PepT2 are major facilitator superfamily (MFS) transporters that utilize a proton gradient to drive the uptake of di- and tri-peptides in the small intestine and kidney, respectively. They are the major routes by which we absorb dietary nitrogen and many orally administered drugs. Here, we present the crystal structure of PepT So, a functionally similar prokaryotic homologue of the mammalian peptide transporters from Shewanella oneidensis. This structure, refined using data up to 3.6 Å resolution, reveals a ligand-bound occluded state for the MFS and provides new insights into a general transport mechanism. We have located the peptide-binding site in a central hydrophilic cavity, which occludes a bound ligand from both sides of the membrane. Residues thought to be involved in proton coupling have also been identified near the extracellular gate of the cavity. Based on these findings and associated kinetic data, we propose that PepT So represents a sound model system for understanding mammalian peptide transport as catalysed by PepT1 and PepT2. © 2011 European Molecular Biology Organization | All Rights Reserved. Hide abstract

Newstead S, Drew D, Cameron AD, Postis VL, Xia X, Fowler PW, Ingram JC, Carpenter EP et al. 2011. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J, 30 (2), pp. 417-426. Read abstract | Read more

PepT1 and PepT2 are major facilitator superfamily (MFS) transporters that utilize a proton gradient to drive the uptake of di- and tri-peptides in the small intestine and kidney, respectively. They are the major routes by which we absorb dietary nitrogen and many orally administered drugs. Here, we present the crystal structure of PepT(So), a functionally similar prokaryotic homologue of the mammalian peptide transporters from Shewanella oneidensis. This structure, refined using data up to 3.6 Å resolution, reveals a ligand-bound occluded state for the MFS and provides new insights into a general transport mechanism. We have located the peptide-binding site in a central hydrophilic cavity, which occludes a bound ligand from both sides of the membrane. Residues thought to be involved in proton coupling have also been identified near the extracellular gate of the cavity. Based on these findings and associated kinetic data, we propose that PepT(So) represents a sound model system for understanding mammalian peptide transport as catalysed by PepT1 and PepT2. Hide abstract

Newstead S, Fowler PW, Bilton P, Carpenter EP, Sadler PJ, Campopiano DJ, Sansom MS, Iwata S. 2009. Insights into how nucleotide-binding domains power ABC transport. Structure, 17 (9), pp. 1213-1222. Read abstract | Read more

The mechanism by which nucleotide-binding domains (NBDs) of ABC transporters power the transport of substrates across cell membranes is currently unclear. Here we report the crystal structure of an NBD, FbpC, from the Neisseria gonorrhoeae ferric iron uptake transporter with an unusual and substantial domain swap in the C-terminal regulatory domain. This entanglement suggests that FbpC is unable to open to the same extent as the homologous protein MalK. Using molecular dynamics we demonstrate that this is not the case: both NBDs open rapidly once ATP is removed. We conclude from this result that the closed structures of FbpC and MalK have higher free energies than their respective open states. This result has important implications for our understanding of the mechanism of power generation in ABC transporters, because the unwinding of this free energy ensures that the opening of these two NBDs is also powered. Hide abstract

Newstead S, Hobbs J, Jordan D, Carpenter EP, Iwata S. 2008. Insights into outer membrane protein crystallization. Mol Membr Biol, 25 (8), pp. 631-638. Read abstract | Read more

Outer membrane proteins are structurally distinct from those that reside in the inner membrane and play important roles in bacterial pathogenicity and human metabolism. X-ray crystallography studies on >40 different outer membrane proteins have revealed that the transmembrane portion of these proteins can be constructed from either beta-sheets or less commonly from alpha-helices. The most common architecture is the beta-barrel, which can be formed from either a single anti-parallel sheet, fused at both ends to form a barrel or from multiple peptide chains. Outer membrane proteins exhibit considerable rigidity and stability, making their study through x-ray crystallography particularly tractable. As the number of structures of outer membrane proteins increases a more rational approach to their crystallization can be made. Herein we analyse the crystallization data from 53 outer membrane proteins and compare the results to those obtained for inner membrane proteins. A targeted sparse matrix screen for outer membrane protein crystallization is presented based on the present analysis. Hide abstract

Weyand S, Shimamura T, Yajima S, Suzuki S, Mirza O, Krusong K, Carpenter EP, Rutherford NG et al. 2008. Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter. Science, 322 (5902), pp. 709-713. Read abstract | Read more

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport. Hide abstract

Carpenter EP, Beis K, Cameron AD, Iwata S. 2008. Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol, 18 (5), pp. 581-586. Read abstract | Read more

Membrane protein structural biology is still a largely unconquered area, given that approximately 25% of all proteins are membrane proteins and yet less than 150 unique structures are available. Membrane proteins have proven to be difficult to study owing to their partially hydrophobic surfaces, flexibility and lack of stability. The field is now taking advantage of the high-throughput revolution in structural biology and methods are emerging for effective expression, solubilisation, purification and crystallisation of membrane proteins. These technical advances will lead to a rapid increase in the rate at which membrane protein structures are solved in the near future. Hide abstract

Electron Microscopy and crystallography of membrane proteins in cancer, metabolic diseases and neuropsychiatric disease

We aim to understand the fundamental causes of diseases such as cancer, metabolic diseases, neuropsychiatric disorders such as autism, bipolar disease and schizophrenia, and inflammation. All of these diseases are caused by failure of cells to make proteins that are properly folded and functional. In the Carpenter lab we study a particularly challenging set of molecules, proteins that are embedded within the membranes of cells and organelles. There are now many studies in progress to identify th ...

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Structural studies of human potassium and calcium channels in pain and heart disease

Ion channels are critical for the function of almost every aspect of the human body, playing essential roles in the brain, nervous system and the heart. Defects in these channels lead to a host of medical conditions such as heart disease, cystic fibrosis and depression. We aim to study these complex, membrane embedded proteins using a range of structure determination techniques (X-ray crystallography, serial femtosecond crystallography, Electron microscopy)  to solve their three dimensional stru ...

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ZMPSTE24, lamin processing and premature ageing: A structure/function study

One of the most serious medical needs for the next 30 years will be to address the adverse consequences of ageing in the general population. A recent UN report predicted that by 2050, 22% of the world’s population will be over age 60. Maintaining physical and mental health, requires increasing intervention with age, with most requiring at least three forms of routine treatment in their 80s. As the population ages the impact on society will increase relentlessly. There is therefore a pressing nee ...

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