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951.
952.
A putative tumor suppressor locus involved in bladder cancer has been mapped to human chromosome 9q32–q33 and designated DBC1. Our previous microsatellite-based deletion mapping study indicated that DBC1 was localized between D9S1848 and AFMA239XA9. We have constructed an 840-kb sequence-ready contig composed of bacteriophage P1-derived artificial chromosomes (PACs), which encompasses DBC1. Clones were initially identified by screening a PAC library with markers localized to the region by physical mapping, and subsequently PAC end probes were used to complete the contig. This contig contains a minimum tiling path of six PAC clones between D9S1848 and AFMA239XA9. Three expressed sequence tags (ESTs) were mapped to the DBC1 region by screening 24 ESTs mapped to the surrounding area by radiation hybrids. One represented the gene for DBCCR1, a known candidate for DBC1, and the other two were novel. This contig and preliminary expression map form the basis for the identification of the bladder cancer tumor suppressor gene in this region. 相似文献
953.
Simian Virus 40 Large T Antigen J Domain and Rb-Binding Motif Are Sufficient To Block Apoptosis Induced by Growth Factor Withdrawal in a Neural Stem Cell Line 总被引:5,自引:0,他引:5
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Serum-free mouse embryo (SFME) cells are a neural stem cell line that is dependent upon epidermal growth factor (EGF) for survival. Removal of EGF results in the G1 arrest and apoptosis of SFME cells. We have shown that the expression of simian virus 40 large T antigen in SFME cells blocks apoptosis and allows cell survival and division in the absence of EGF. Therefore the presence of T antigen abrogates the EGF requirement. The steady-state levels of p53, p21, and mdm-2 do not increase as SFME cells undergo apoptosis upon EGF withdrawal. Furthermore, the amino-terminal 136 amino acids (N136) of T antigen are sufficient to block death and to promote proliferation in the absence of EGF, while the carboxy-terminal fragment (C251-708), which contains the p53 binding site, is unable to block death. Taken together, these data suggest that SFME cells deprived of EGF undergo p53-independent apoptosis. Mutations that disrupt either the J domain or Rb family binding abolish the ability of T antigen to block SFME cell apoptosis and to promote cell growth. We conclude that T antigen must act on one or more members of the Rb family to inhibit SFME cell apoptosis. 相似文献
954.
Effects of Targeting Herpes Simplex Virus Type 1 gD to the Endoplasmic Reticulum and trans-Golgi Network
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Glycoprotein D (gD) of herpes simplex virus type 1 (HSV-1) was modified to encode targeting signals known to localize proteins to either the endoplasmic reticulum (ER) or the trans-Golgi network. These motifs conferred the predicted targeting properties on gD in transfected cells as judged by immunofluorescence staining, and the exclusion of targeted gD from the cell surface was confirmed by the fact that these molecules exhibited substantially reduced activity in cell-cell fusion assays. Recombinant viruses expressing Golgi-targeted forms of gD grew to wild-type levels in noncomplementing cells, exhibited unaltered particle/infectivity ratios, and were found to contain wild-type levels of gD, whereas a recombinant expressing ER-retained gD was helper cell dependent and, when grown on noncomplementing cells, produced virions of low specific infectivity with greatly reduced levels of gD. These data imply that HSV-1 acquires its final membrane from a post-ER compartment and lend support to the view that the virus undergoes de-envelopment and reenvelopment steps during virus egress. 相似文献
955.
956.
Although females are traditionally thought of as the choosy sex, there is increasing evidence in many species that males will preferentially court or mate with certain females over others when given a choice. In the fruit fly, Drosophila melanogaster, males discriminate between potential mating partners based on a number of female traits, including species, mating history, age, and condition. Interestingly, many of these male preferences are affected by the male''s previous sexual experiences, such that males increase courtship toward types of females that they have previously mated with and decrease courtship toward types of females that have previously rejected them. D. melanogaster males also show courtship and mating preferences for larger females over smaller females, likely because larger females have higher fecundity. It is unknown, however, whether this preference shows behavioral plasticity based on the male''s sexual history as we see for other male preferences. Here, we manipulate the sexual experience of D. melanogaster males and test whether this manipulation has any effect on the strength of male mate choice for large females. We find that sexually inexperienced males have a robust courtship preference for large females that is unaffected by previous experience mating with, or being rejected by, females of differing sizes. Given that female body size is one of the most common targets of male mate choice across insect species, our experiments with D. melanogaster may provide insight into how these preferences develop and evolve. 相似文献
957.
Matthew A. Ismail Karen J. Sanders Gareth C. Fennell Harriet C. Latham Paul Wormell Alison Rodger 《Biopolymers》1998,46(3):127-143
The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127–143, 1998 相似文献
958.
Daniel T. Infield Kerry M. Strickland Amit Gaggar Nael A. McCarty 《The Journal of general physiology》2021,153(12)
The ATP-binding cassette (ABC) transporter superfamily includes many proteins of clinical relevance, with genes expressed in all domains of life. Although most members use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes, the cystic fibrosis transmembrane conductance regulator (CFTR) is the only known animal ABC transporter that functions primarily as an ion channel. Defects in CFTR, which is closely related to ABCC subfamily members that bear function as bona fide transporters, underlie the lethal genetic disease cystic fibrosis. This article seeks to integrate structural, functional, and genomic data to begin to answer the critical question of how the function of CFTR evolved to exhibit regulated channel activity. We highlight several examples wherein preexisting features in ABCC transporters were functionally leveraged as is, or altered by molecular evolution, to ultimately support channel function. This includes features that may underlie (1) construction of an anionic channel pore from an anionic substrate transport pathway, (2) establishment and tuning of phosphoregulation, and (3) optimization of channel function by specialized ligand–channel interactions. We also discuss how divergence and conservation may help elucidate the pharmacology of important CFTR modulators.IntroductionThe ATP-binding cassette (ABC) transporter superfamily includes many members of clinical relevance, such as the multidrug resistance proteins (MRPs) and other proteins involved in generation of antibiotic resistance, transport of a wide variety of substrates in pathogenic bacteria, and transport of bile acids, lipids, and lipopolysaccharides (Ford and Beis, 2019; Jetter and Kullak-Ublick, 2020). ABC transporter genes encode the largest family of transmembrane (TM) proteins among living organisms (Briz et al., 2019) and are expressed in all domains of life (Ford and Beis, 2019; Holland et al., 2003). Either function or dysfunction of ABC transporters is implicated in development or treatment of cancer (Briz et al., 2019; Nobili et al., 2020), neurological disorders (Jha et al., 2019; Sumirtanurdin et al., 2019), detoxification (Briz et al., 2019), visual function (Garces et al., 2018), and, among many other clinical presentations (Moitra and Dean, 2011), in cystic fibrosis (CF; Riordan et al., 1989). In CF, mutations in the gene encoding CFTR lead to loss of anion transport in a wide variety of epithelial tissues (Csanády et al., 2019). In this review, we use the data generated from >30 yr of intensive structure-function study of CFTR and related proteins to propose and evaluate a potential route by which CFTR may have evolved unique function as a phosphorylation-regulated chloride channel. New insights are made possible by the advent of high-resolution cryo-EM structures of CFTR and the recent cloning and characterization of the evolutionarily oldest known orthologue of CFTR, from sea lamprey (Lp-CFTR; see below), which exhibits many functional differences from the human CFTR orthologue (hCFTR; Cui et al., 2019a).Overview of CFTRCFTR is a Cl−/HCO3− channel whose dysfunction directly leads to CF, the most common life-shortening genetic disease among Caucasians, affecting ∼80,000 individuals worldwide (Riordan et al., 1989; https://cftr2.org/mutations_history). The role of CFTR has been well characterized in airway, intestine, and sweat gland epithelial cells (Buchwald et al., 1991; Gonska et al., 2009; Haq et al., 2016; Quinton et al., 2012; Quinton, 2007; Trezíse and Buchwald, 1991), where the anionic flux mediated by the protein contributes to water secretion and regulation of pH (Pezzulo et al., 2012; Rowe et al., 2014). CFTR also functions in several nonepithelial cell types (Cook et al., 2016; Edlund et al., 2014; Gao and Su, 2015; Guo et al., 2014; Norez et al., 2014; Pohl et al., 2014; Schulz and Tümmler, 2016; Su et al., 2011), including in the brain (Ballerini et al., 2002; Guo et al., 2009; Hincke et al., 1995; Johannesson et al., 1997; Mulberg et al., 1995; Mulberg et al., 1998; Parkerson and Sontheimer, 2004; Pfister et al., 2015; Plog et al., 2010; Weyler et al., 1999). Several hundred disease-causing mutations have been identified in the CFTR gene. For a subset of these mutations, four small-molecule modulator therapeutics from Vertex Pharmaceuticals, Inc. that increase the surface expression or activity of CFTR have been approved for clinical use. The first approved drug, VX-770 (ivacaftor), is a gating potentiator that increases function of certain CFTR mutants (Cui et al., 2019b; Sosnay et al., 2013; Van Goor et al., 2009; Van Goor et al., 2014; Yu et al., 2012). A better understanding of these drugs and their binding sites may aid in refining the next class of therapeutics.ABC transporters use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes (Rees et al., 2009). There are seven subfamilies of mammalian ABC transporters (ABCA, ABCB, ABCC,… ABCG), of which the E and F subfamilies do not bear actual transport function (Dean et al., 2001; Ford and Beis, 2019). A new classification of the ABC transporter superfamily that is based on the transmembrane domain (TMD) fold has recently been suggested (Thomas et al., 2020). CFTR is denoted ABCC7 and a member of type IV, respectively, according to these two classification schemes. CFTR bears ATPase activity like that of other ABCC subfamily members (Li et al., 1996; Stratford et al., 2007; Jordan et al., 2008), but biophysical methods have firmly established that CFTR functions as a phosphorylation-activated and ATP-gated ion channel (Anderson et al., 1991a; Anderson et al., 1991b; Bear et al., 1992; Berger et al., 1991; Sheppard et al., 1993), whereas its closest ABCC relatives function as multispecific exporters of organic anions (Jordan et al., 2008). CFTR may directly mediate the flux of glutathione (Gao et al., 1999; Kogan et al., 2003; Linsdell and Hanrahan, 1998), although CFTR-mediated active transport has not been shown, to our knowledge. Glutathione is transported by close ABCC relatives ABCC1/MRP1 (Mao et al., 1999) and ABCC4/MRP4 (Choi et al., 2001; Ko et al., 2002; Kogan et al., 2003; Ritter et al., 2005; Serrano et al., 2006); previous analysis has identified ABCC4 as CFTR’s closest relative (Jordan et al., 2008; see also Cui et al., 2019a). The domain organization of CFTR is similar to that of its closest relatives, the “short transporters” of the ABCC subfamily (Jordan et al., 2008; Ford and Beis, 2019; Srikant and Gaudet, 2019), with two nucleotide-binding domains (NBDs) that function in ATP binding and hydrolysis, and two TMDs, each containing six TM helices that comprise the substrate transport pathway (Fig. 1). However, unique to CFTR is an intracellular regulatory (R) domain that contains multiple consensus sites for phosphorylation by PKA (Sebastian et al., 2013).Open in a separate windowFigure 1.Domain architecture of CFTR. (A) Five functional domains: TMD1, NBD1, R domain with multiple phosphorylation sites, TMD2, and NBD2. Each TMD includes six transmembrane helices, numbered 1–12. The N-terminus includes the lasso motif (shown in pink), whereas the C-terminus includes a PDZ binding domain motif (yellow). (B) hCFTR from cryo-EM structure (PDB accession no. 6MSM). The R domain is not shown, because it is intrinsically unstructured.The opening of CFTR may be simplified to involve three sequential steps that have been uncovered via a combination of functional and structural data. First, PKA binds to (Mihályi et al., 2020) and phosphorylates (Rich et al., 1991) the aforementioned R domain, which results in loss of inhibitory interactions between that domain and the rest of the channel protein. Second, ATP binds to two sites at the interface of the cytoplasmic NBDs, which promotes a stable NBD dimer (Mense et al., 2006; Vergani et al., 2005). Finally, the wave of conformational changes associated with ATP-induced dimerization of the NBDs is transmitted to the pore domain, resulting in pore opening (Rahman et al., 2013; Simhaev et al., 2017; Sorum et al., 2015; Strickland et al., 2019). In related ABC exporters, ATP-dependent dimerization of the NBDs drives an overall transition from inward- to outward-facing conformation of the TMDs; this function was coopted by CFTR to drive ATP-induced channel opening (Fig. 2). At the level of individual residues, there is high conservation with transporters among amino acids in CFTR that are proposed to stabilize the inward-facing (closed) conformation in the absence of ATP (Wang et al., 2010; Wei et al., 2014; Wei et al., 2016), suggesting conservation of motifs integral to energetic signaling (Wang et al., 2014b; Wei et al., 2014; Wei et al., 2016). The close proximity of intracellular loops 2 and 4 (ICL2 and ICL4, respectively; Doshi et al., 2013; Wang et al., 2014b), constriction of the intracellular vestibule (Bai et al., 2011), and dilation of the extracellular vestibule, relative to the closed state, are all associated with channel opening (Beck et al., 2008; Infield et al., 2016; Norimatsu et al., 2012b; Rahman et al., 2013; Strickland et al., 2019). The CFTR pore opens in stages, requiring the sequential breaking and forming of intraprotein residue–residue interactions (Cui et al., 2013, 2014; Rahman et al., 2013), resulting in two subconductance states in addition to the full-conductance state (Gunderson and Kopito, 1995; Zhang et al., 2005a; Zhang et al., 2005b; Fig. 3). Using a particularly informative cysteine mutant at the outer vestibule, R334C-CFTR, the McCarty laboratory found that transitions between these subconductance states are highly dependent upon experimental conditions; for example, closing transitions almost always start from the s2 state in the presence of ATP, and transitions from s2 to f never occur in channels bound with the poorly hydrolyzable ATP analogue AMP-PNP (see also Langron et al., 2018), suggesting that this transition requires hydrolysis of nucleotide at the NBDs (Zhang et al., 2005a; Zhang et al., 2005b). Subconductance states are evident in recordings of WT CFTR from membrane patches and planar lipid bilayers, depending on experimental conditions, indicating that these represent inherent steps in gating of the channel pore (Gunderson and Kopito, 1995). In WT-hCFTR, this open pore is quite stable and does not close until ATP is hydrolyzed at the NBDs (Baukrowitz et al., 1994). Note that because CFTR displays three types of gating in one channel (phosphorylation-mediated, ligand-mediated, and pore-mediated gating), it serves as an exemplary target for studying the evolution of functional mechanisms within a single membrane protein.Open in a separate windowFigure 2.Hypothesis for emergence of channel function in CFTR. Modification of ATP-dependent transport activity in ABC transporters led to channel behavior, coopting the conformational changes necessary for unidirectional substrate transport in common ABC transporter systems. CFTR evolved features that break the alternating access cycle (solid-line arrows), enabling it to be open at both ends (box). Color scheme for major domains (again, lacking the R domain) is the same as in Fig. 1.Open in a separate windowFigure 3.Gating scheme for CFTR. Prephosphorylated channels are shown in the membrane (gray slab) with two TMDs (brown and dark blue) and two NBDs (green and light blue), with ATP (red circle) and ADP (yellow circle). ATP-dependent gating is shown as including NBD-mediated gating steps leading to pore gating between conductance levels. Here, we do not distinguish between s1 and s2 subconductance levels, because s1→s2 occurs very rapidly in WT-hCFTR.Natural history of the CFTR channel in vertebratesGiven the structural conservation among CFTR and ABC exporters noted above, and functional conservation in terms of ATP dependence, how CFTR evolved to function as an anion channel regulating passive ionic diffusion has been an enduring question (Srikant, 2020; Srikant et al., 2020). Molecular evolution studies are facilitated by the availability of many orthologues for the protein/gene of interest, spanning as much of the evolutionary record as possible. Currently, ∼300 CFTR orthologues are included in GenBank/UniProt, although not all of these are represented by expressible cDNA clones. Until very recently, the oldest CFTR orthologue known was from the dogfish shark, arising ∼150 million yr ago (MYA; Fig. 4; Marshall et al., 1991); this orthologue bears functional characteristics similar to those of hCFTR. However, reasoning that the identification of an earlier CFTR orthologue with altered structure/function would provide novel insight into the evolution of epithelial anion transport, the Gaggar and McCarty laboratories recently led an effort to clone and characterize the Lp-CFTR (Cui et al., 2019a), which arose ∼550 MYA (Smith et al., 2013). The identification of a CFTR orthologue in the jawless vertebrates establishes that CFTR exists across all vertebrates, predating the divergence of jawed and jawless vertebrates at the end of the Cambrian Period ∼488 MYA. Sequence analysis indicates 46% sequence identity and 65% sequence similarity between Lp-CFTR and hCFTR, which is much lower than that among jawed vertebrate CFTRs (jv-CFTRs) and includes surprising divergence in functionally relevant motifs. Accordingly, Lp-CFTR differs from hCFTR in multiple functional characteristics (Fig. 4). Thus, it cannot be automatically assumed that every position in CFTR that is unique in sea lamprey represents transitional change in the development of regulated channel activity. A good example in this regard is that of F508 in hCFTR, which is conserved across multiple ABC proteins but is leucine in lamprey (Cui et al., 2019a). Sorum et al. (2017) showed that replacing F508 with L in hCFTR significantly reduced its open probability. All known CFTRs other than Lp-CFTR and all known human ABCCs have F at this position, where the aromatic side chain is necessary for stabilizing the outward-facing state (Cui et al., 2006), so finding that this is substituted by a nonaromatic side chain in Lp-CFTR is mechanistically interesting and may represent a species-specific adaptation (Cui et al., 2019a).Open in a separate windowFigure 4.Simplified and truncated evolutionary tree for vertebrates. Green, common vertebrate ancestor; blue, jawless vertebrates; red and yellow, jawed vertebrates; yellow, mammals. CFTR orthologues studied in functional assays are shown underlined. (The time domain in this figure is not implied.)Table 1.Comparison of features between human and lamprey orthologues, focusing on three major domains of function: channel behavior, regulation, and modulation
Open in a separate windowNPPB, 5-nitro-2-(3-phenyl-propylamino) benzoic acid. Related to Cui et al., 2019a.Below, we identify several potential routes by which CFTR evolved regulated channel behavior. We propose that many features shared among bona fide ABCC proteins and present in recent ABCC ancestors of CFTR provided a unique opportunity for emergence of novel channel function by incremental evolutionary changes.Molecular evolution of channel functionConstruction of an anionic pore from an anionic substrate pathwayBoth the passive conduction of anions by CFTR and the unidirectional transport of highly structurally diverse organic anions by its ABCC relatives (Sauna et al., 2004) is accomplished by pathways through the TMDs. Therefore, divergence in these pathways would be expected to most closely reflect the principal difference between channels and transporters: channels contain a pore that allows uninterrupted permeation across the plasma membrane, a violation of the “alternating access” mechanism of transporters (Fig. 2; Bai et al., 2011; Gadsby, 2009). This divergence would be accomplished by evolutionary changes distributed broadly through the TMDs, as suggested by a recent study of mutations that alter substrate specificity in a fungal pheromone transporter (Srikant and Gaudet, 2019; Srikant et al., 2020). In formation of the CFTR chloride channel, this would require both degradation of the “gates” seen in ABC transporters and stabilization of an open pore conformation (Bai et al., 2011). The relationship between substrate binding and opening/closure of these gates, relevant to establishing the occluded state in transporters, may remain in CFTR in a vestigial state, as evidenced by reports that permeating anions may affect gating transitions (Sorum et al., 2015; Yeh et al., 2015; Zhang et al., 2000; Zhang et al., 2002).Understanding how the CFTR pore evolved requires the integration of functional and structural information. Early 2-D electron crystallography of hCFTR at low resolution (Rosenberg et al., 2004; Rosenberg et al., 2011) confirmed the general ABC-like architecture of CFTR predicted in the initial gene discovery study (Riordan et al., 1989). In addition, several homology models of CFTR were developed using structures of related ABC transporters as a template. These studies contributed to the understanding of the molecular interface encompassing the most common CF-causing mutation (ΔF508; Mornon et al., 2008; Serohijos et al., 2008), as well as several details relating to the conformational transitions underlying CFTR gating (Corradi et al., 2015; Dalton et al., 2012; Furukawa-Hagiya et al., 2013; Mornon et al., 2015; Mornon et al., 2009; Rahman et al., 2013; Strickland et al., 2019). However, the disparity between the wide variety of substrates of nonchannel ABC transporters and the chloride channel function of CFTR resulted in intrinsically limited confidence in these homology models, at least with respect to the TMDs.In the last 5 yr, eight structures of detergent-solubilized CFTR from three orthologues have been released from two laboratories in a large range of resolutions, all solved by single-particle cryo-EM (Fig. 5).Table 2.High-resolution CFTR structures to date
Open in a separate windowch, chicken; CHS, cholesteryl hemisuccinate; DMNG, decyl maltose neopentyl glycol; LMNG, lauryl maltose neopentyl glycol; zf, zebrafish.Open in a separate windowFigure 5.High-resolution structures of CFTR. See Liu et al., 2017; Zhang and Chen, 2016). Subsequently, the structures of phosphorylated, ATP-bound, hydrolysis-deficient mutants of zfCFTR and hCFTR in the outward-facing state were resolved at reported resolutions of 3.4 Å and 3.2 Å, respectively (Zhang et al., 2017; Zhang et al., 2018). In addition to revealing a structural motif unsuspected for CFTR—the lasso motif found in other ABCC transporters (e.g., SUR1, SUR2, MRP1) in which the N-terminus loops into the lipid bilayer (Fig. 1 A)—these CFTR structures exhibited TM helix positioning and secondary structure that may be unique to CFTR among the ABCs. Of note, TM7 and TM8 are rearranged such that the top-down TM helix symmetry of most ABC transporters is broken. There are also kinks in TM8 and TM5 helices in approximately the same vertical position. We note that two structures from recombinant thermostabilized chicken CFTR (chCFTR), one in dephosphorylated conditions with ATP present (resolution, 4.3 Å) and one in phosphorylated conditions with ATP present (resolution, 6.6 Å), show TM8 as fully helical and lack the rearrangement of TM7 and TM8, instead positioning TM7 nearly orthogonal to the fatty acid tails of the lipid bilayer (see Fig. 5; Fay et al., 2018).The positioning of TM8 in the Chen structures has been supported by functional evidence suggesting that some residues of TM8 line the CFTR channel pore (Negoda et al., 2019). The unwound portion of TM8 has been proposed by the Chen laboratory to underlie CFTR’s unique channel function (Liu et al., 2017), and molecular dynamics studies suggest that this unwinding would be maintained in a lipid bilayer (Corradi et al., 2018). The stability of this segment may be enhanced by interactions between R933, located at the intracellular boundary of the unwound portion of TM8, and E873, in TM7. In both the structures of closed hCFTR (Protein Data Bank [PDB] accession no. 5UAK) and nearly open hCFTR with ATP bound (PDB accession no. 6MSM), the oppositely charged ends of these residues essentially overlap. It is very interesting to note that R933 is conserved within CFTR and ABCC4 orthologues among both jawed and jawless vertebrates. However, E873 is conserved within jawed vertebrates but is Q in both Lp-CFTR and all ABCC4s, although this assignment must remain tentative due to the poor alignment between CFTR and ABCC4 sequences in TM7. Within the unwound stretch of TM8 itself, sequences are poorly conserved even within the CFTR and ABCC4 branches.Importantly, an open structure of CFTR with a fully conducting ion pore has yet to be published. Currently, all structures have been determined with CFTR in detergent; additional structures of CFTR in a lipidic environment may be needed to elucidate the fully conducting ion pathway as well as to understand the complex conformational transitions between open and closed states. Regardless of these considerations, these structures can certainly be used to spatially locate amino acids that have been implicated in CFTR channel function. In aid of this, significant effort has been expended to functionally map the chloride conduction pathway through CFTR. Many studies have mutated putative pore residues and characterized channel behavior and modulation (Linsdell et al., 1997; McCarty et al., 1993; McDonough et al., 1994; Tabcharani et al., 1997). To identify explicitly “pore-lining” residues, several groups have employed the substituted cysteine accessibility method. This approach probes the environment of specific residues by mutating them to cysteine and characterizing their reaction to sulfhydryl-specific chemicals (Karlin and Akabas, 1998).In the process of going through the channel to exit the cell, the chloride ion first encounters highly conserved basic residues in the ICLs, including K190, R248, R303, K370, R1030, K1041, and R1048. These residues are proposed to play roles in attracting chloride ions into the pore because charge-eliminating mutations reduce single-channel conductance (Aubin and Linsdell, 2006; El Hiani and Linsdell, 2015; Zhou et al., 2008). Considering that they mediate anion conduction, it is initially surprising that this group of residues is very highly conserved in transporter ABCCs: all seven residues analogous to those listed above are basic in ABCC4 and most (five of seven) are basic in ABCC5. To our knowledge, the effect of mutations at these positions on the function of ABCC4 or ABCC5 has not been directly tested. However, functional studies of MRP1 (ABCC1) have specifically implicated several basic residues in analogous regions in the binding of organic anionic substrates (Conseil et al., 2006; Haimeur et al., 2004) that are transported by the majority of ABCCs, including ABCC4 and ABCC5 (Jansen et al., 2015; Ritter et al., 2005). These data are intriguing because they suggest that one way in which CFTR evolved chloride channel activity was to use residues already functionally important in the transport of organic anionic substrates and repurpose them toward the novel function of conducting inorganic anions through the channel pore. In further support of this, several substrates of ABCC transporters inhibit CFTR by blocking the pore from the intracellular side (Linsdell and Hanrahan, 1999). Hence, these residues may contribute to a vestigial binding site for these substrates within CFTR. Another intriguing possibility is that ABCC4 and ABCC5 may allow the conductance of chloride along with their traditional substrates during transport, in a manner akin to the leak current associated with the function of neurotransmitter transporters (Fairman et al., 1995; Sonders and Amara, 1996; Wadiche et al., 1995). Such a substrate-induced current has not yet been measured from cells expressing ABCC4 or ABCC5, although this would be expected to be of very low amplitude (due to the slower nature of transporter function) and would likely be challenging to measure because substrate binds intracellularly in these proteins.As the chloride ion travels further up the CFTR pore toward the extracellular space, it encounters pore-lining residues contributed by TM helices 1, 5, 6, 8, 9, 11, and 12 (Alexander et al., 2009; Bai et al., 2010; Bai et al., 2011; Gao et al., 2013; McDonough et al., 1994; Wang et al., 2014a; Zhang and Hwang, 2015; Zhang et al., 2005b; Zhang et al., 2002). Fig. 6 A shows the nearly open structure of hCFTR, wherein we have highlighted residues shown by the substituted cysteine accessibility method to line the pore (Akabas, 1998; Alexander et al., 2009; Aubin and Linsdell, 2006; Bai et al., 2010; Bai et al., 2011; El Hiani and Linsdell, 2015; El Hiani et al., 2016; Fatehi and Linsdell, 2009; Gao et al., 2013; Liu et al., 2004; Negoda et al., 2019; Norimatsu et al., 2012a; Norimatsu et al., 2012b; Qian et al., 2011; Rubaiy and Linsdell, 2015; Serrano et al., 2006; Wang et al., 2011; Wang et al., 2014a; Zhang and Hwang, 2015; Zhou et al., 2008). Residues are colored according to conservation between CFTR and ABCC4 (Jordan et al., 2008; dark blue, conserved; black, similar; magenta, divergent).Open in a separate windowFigure 6.Conservation with ABCC4 in residues lining the CFTR channel pore. (A) hCFTR structure (PDB accession no. 6MSM) in nearly open state, showing major domains, with sections of non–pore-lining helices removed in order to visualize the chloride ion permeation pathway. Dark blue residues, identical between jawed vertebrate consensus CFTR and ABCC4; black residues, biochemically similar; magenta, biochemically divergent. The highly divergent pore-lining TM6 is bounded in red. (B) hCFTR (PDB accession no. 6MSM) is again shown, highlighting a lateral portal proposed to enable unique chloride channel activity among ABCCs. Inset is a closeup view of a kink in TM6. P355 is conserved with ABCC4, whereas R352 and Q353 are divergent.Strikingly, the pore-lining residues of several TMs are highly conserved between CFTR and ABCC4; for example, in TM1, six of seven pore-lining residues in CFTR are identical in ABCC4. Regarding this conservation, TM6 (see region bounded in red in Fig. 6) is an outlier, both in terms of the number of biochemically divergent pore-lining residues and as calculated as a sum of the Grantham scores (incorporating differences in composition, polarity, and molecular volume; Grantham, 1974) to gauge evolutionary distance between consensus amino acids of CFTR and ABCC4 sequences from jawed vertebrates (Alexander et al., 2009; Bai et al., 2010; Norimatsu et al., 2012a), whereas residues F337 through V345 exhibit a helical pattern of modification by MTS reagents applied intracellularly (Bai et al., 2010; El Hiani and Linsdell, 2010). This also contrasts with better-conserved helices such as TM1 and TM11, wherein reactivity follows a helical periodicity (Region Residue numbers Aggregate Grantham scorea TM1 92, 95, 98, 102, 106, 107, 109 111 ICL1 186, 188, 189, 190, 32 TM3 191, 192, 193, 194, 195, 196, 197, 199, 200, 203, 205, 207, 211, 213, 215 532 ICL2 241, 243, 244, 248, 252, 299, 303, 142 TM5 306, 307, 310, 311, 326 209 TM6 331, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 344, 345, 348, 349, 352, 353, 355, 356, 360, 367, 370 1,389 TM8 913, 914, 917 327 ICL3 986, 988, 989, 990 0 TM9 993, 1000, 1003, 1008, 1009, 1010 361 ICL4 1030, 1041, 1048 0 TM11 1112, 1115, 1118 58 TM12 1127, 1129, 1131, 1132, 1134, 1135, 1137, 1138, 1139, 1140, 1141, 1142, 1144, 1145, 1147, 1148, 1150, 1152, 1156 561
Lp-CFTR | hCFTR | |
---|---|---|
Functional domain: channel behavior | ||
Open channel stability (open burst duration) | Low | High |
Frequency of subconductance states | High | Low |
Single-channel open conductance | Low | High |
Shape of I-V relationship | Rectified | Linear |
Sensitivity to (affinity for) ATP for channel opening | Very low | High |
Functional domain: regulation by phosphorylation | ||
Rate of activation by PKA-mediated phosphorylation | Low | High |
Number of predicted PKA sites in the R domain | 4 | 8 |
Functional domain: pharmacological modulation | ||
Effect of VX-770/ivacaftor (inhibition versus potentiation) | Small inhibition | Potentiation |
Inhibition by CFTRinh172 | Low | High |
Sensitivity to pore block by GlyH-101 | None | High |
Sensitivity to pore block by NPPB | Low | High |
Sensitivity to pore block by glibenclamide | Equal | Equal |
Protein | zfCFTR | hCFTR | zfCFTR | hCFTR | hCFTR | hCFTR | chCFTR | chCFTR |
---|---|---|---|---|---|---|---|---|
Orthologue | Zebrafish | Human | Zebrafish | Human | Human | Human | Chicken | Chicken |
Resolution | 3.7 Å | 3.9 Å | 3.4 Å | 3.2 Å | 3.3 Å | 3.2 Å | 4.3 Å | 6.6 Å |
Detergent | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (LMNG, digitonin, CHS) | Detergent (DMNG, digitonin) | Detergent (DMNG, digitonin) |
Mutation | – | – | E1372Q | E1371Q | E1371Q | E1371Q | ΔRI/1404S/1441X | ΔRI/1404S/1441X |
State | Closed, inward facing, dephosphorylated, apo-ATP | Closed, inward facing, dephosphorylated, apo-ATP | Closed, outward facing, phosphorylated, ATP-bound | Closed, outward facing, Phosphorylated, ATP-bound | Closed, outward facing, Phosphorylated, ATP-bound, VX-770-bound | Closed, outward facing, Phosphorylated, ATP-bound, GLPG1837-bound | Closed, inward facing, dephosphorylated, ATP-present | Closed, inward facing, phosphorylated, ATP-present |
PDB accession no. | 5UAR | 5UAK | 5W81 | 6MSM | 6O2P | 6O1V | 6D3R | 6D3S |
Year | 2016 | 2017 | 2017 | 2018 | 2019 | 2019 | 2018 | 2018 |