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Chikunova A, Manley MP, Heijjer CN, Drenth CS, Cramer-Blok AJ, Ahmad MUD, Perrakis A, Ubbink M. Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC. Protein Sci 2024; 33:e4972. [PMID: 38533527 DOI: 10.1002/pro.4972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Evolution leads to conservation of amino acid residues in protein families. Conserved proline residues are usually considered to ensure the correct folding and to stabilize the three-dimensional structure. Surprisingly, proline residues that are highly conserved in class A β-lactamases were found to tolerate various substitutions without large losses in enzyme activity. We investigated the roles of three conserved prolines at positions 107, 226, and 258 in the β-lactamase BlaC from Mycobacterium tuberculosis and found that mutations can lead to dimerization of the enzyme and an overall less stable protein that is prone to aggregate over time. For the variant Pro107Thr, the crystal structure shows dimer formation resembling domain swapping. It is concluded that the proline substitutions loosen the structure, enhancing multimerization. Even though the enzyme does not lose its properties without the conserved proline residues, the prolines ensure the long-term structural integrity of the enzyme.
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Affiliation(s)
- A Chikunova
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - M P Manley
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - C N Heijjer
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - C S Drenth
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - A J Cramer-Blok
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - M Ud Din Ahmad
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A Perrakis
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M Ubbink
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Department of Infectious Diseases, Imperial College, London, UK
- Zocdoc, New York City, New York, USA
- ZoBio BV, Leiden, The Netherlands
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2
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Sauer DB, Song J, Wang B, Hilton JK, Karpowich NK, Mindell JA, Rice WJ, Wang DN. Structure and inhibition mechanism of the human citrate transporter NaCT. Nature 2021; 591:157-161. [PMID: 33597751 PMCID: PMC7933130 DOI: 10.1038/s41586-021-03230-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022]
Abstract
Citrate is most well-known as an intermediate in the TCA cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis 1–3. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic citrate concentration 4,5. Liver cells import citrate via the sodium-dependent citrate transporter NaCT (SLC13A5), and as a consequence this protein is a potential target for anti-obesity drugs. To understand the structural basis of its inhibition mechanism, we have determined cryo-electron microscopy structures of human NaCT in complex with citrate and with a small molecule inhibitor. These structures reveal how the inhibitor, bound at the same site as citrate, arrests the protein’s transport cycle. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish NaCT’s transport activity in the brain and thereby cause SLC13A5-Epilepsy in newborns 6–8.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Jacob K Hilton
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nathan K Karpowich
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.,Janssen Pharmaceuticals, Spring House, PA, USA
| | - Joseph A Mindell
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - William J Rice
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA. .,Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA.
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA. .,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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3
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Klotz J, Porter BE, Colas C, Schlessinger A, Pajor AM. Mutations in the Na(+)/citrate cotransporter NaCT (SLC13A5) in pediatric patients with epilepsy and developmental delay. Mol Med 2016; 22:molmed.2016.00077. [PMID: 27261973 DOI: 10.2119/molmed.2016.00077] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 01/13/2023] Open
Abstract
Mutations in the SLC13A5 gene that codes for the Na(+)/citrate cotransporter, NaCT, are associated with early onset epilepsy, developmental delay and tooth dysplasia in children. In the present study we identify additional SLC13A5 mutations in nine epilepsy patients from six families. To better characterize the syndrome, families with affected children answered questions about the scope of illness and treatment strategies. There are currently no effective treatments, but some anti-epileptic drugs targeting the GABA system reduce seizure frequency. Acetazolamide, a carbonic anhydrase inhibitor and atypical anti-seizure medication decreases seizures in 4 patients. In contrast to previous reports, the ketogenic diet and fasting produce worsening of symptoms. The effects of the mutations on NaCT transport function and protein expression were examined by transient transfections of COS-7 cells. There was no transport activity from any of the mutant transporters, although some of the mutant transporter proteins were present on the plasma membrane. The structural model of NaCT suggests that these mutations can affect helix packing or substrate binding. We tested various treatments, including chemical chaperones and low temperatures, but none improve transport function in the NaCT mutants. Interestingly, coexpression of NaCT and the mutants results in decreased protein expression and activity of the wild-type transporter, indicating functional interaction. In conclusion, our study has identified additional SLC13A5 mutations in patients with chronic epilepsy starting in the neonatal period, with the mutations producing inactive Na(+)/citrate transporters.
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Affiliation(s)
- Jenna Klotz
- Department of Neurology, Stanford University School of Medicine, Palo Alto, CA 94305
| | - Brenda E Porter
- Department of Neurology, Stanford University School of Medicine, Palo Alto, CA 94305
| | - Claire Colas
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Avner Schlessinger
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92130-0718
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4
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Mancusso R, Gregorio GG, Liu Q, Wang DN. Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter. Nature 2012; 491:622-6. [PMID: 23086149 DOI: 10.1038/nature11542] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/30/2012] [Indexed: 01/01/2023]
Abstract
In human cells, cytosolic citrate is a chief precursor for the synthesis of fatty acids, triacylglycerols, cholesterol and low-density lipoprotein. Cytosolic citrate further regulates the energy balance of the cell by activating the fatty-acid-synthesis pathway while downregulating both the glycolysis and fatty-acid β-oxidation pathways. The rate of fatty-acid synthesis in liver and adipose cells, the two main tissue types for such synthesis, correlates directly with the concentration of citrate in the cytosol, with the cytosolic citrate concentration partially depending on direct import across the plasma membrane through the Na(+)-dependent citrate transporter (NaCT). Mutations of the homologous fly gene (Indy; I'm not dead yet) result in reduced fat storage through calorie restriction. More recently, Nact (also known as Slc13a5)-knockout mice have been found to have increased hepatic mitochondrial biogenesis, higher lipid oxidation and energy expenditure, and reduced lipogenesis, which taken together protect the mice from obesity and insulin resistance. To understand the transport mechanism of NaCT and INDY proteins, here we report the 3.2 Å crystal structure of a bacterial INDY homologue. One citrate molecule and one sodium ion are bound per protein, and their binding sites are defined by conserved amino acid motifs, forming the structural basis for understanding the specificity of the transporter. Comparison of the structures of the two symmetrical halves of the transporter suggests conformational changes that propel substrate translocation.
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Affiliation(s)
- Romina Mancusso
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA
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5
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Cory AT, Price CA, Lefebvre R, Palin MF. Identification of single nucleotide polymorphisms in the bovine follicle-stimulating hormone receptor and effects of genotypes on superovulatory response traits. Anim Genet 2012; 44:197-201. [DOI: 10.1111/j.1365-2052.2012.02380.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Aron T. Cory
- Centre de Recherche en Reproduction Animale, Faculté de Médecine Vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
| | - Christopher A. Price
- Centre de Recherche en Reproduction Animale, Faculté de Médecine Vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
| | - Rejean Lefebvre
- Centre de Recherche en Reproduction Animale, Faculté de Médecine Vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
- Department of Clinical science, Faculté de Médecine Vétérinaire; Université de Montréal; St-Hyacinthe QC Canada
| | - Marie-France Palin
- Dairy and Swine Research and Development Centre; Agriculture and Agri-Food Canada; Sherbrooke QC Canada
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6
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Pajor AM, Sun NN, Joshi AD, Randolph KM. Transmembrane helix 7 in the Na+/dicarboxylate cotransporter 1 is an outer helix that contains residues critical for function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:1454-61. [PMID: 21073858 DOI: 10.1016/j.bbamem.2010.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 11/02/2010] [Accepted: 11/04/2010] [Indexed: 11/30/2022]
Abstract
Citric acid cycle intermediates, including succinate and citrate, are absorbed across the apical membrane by the NaDC1 Na+/dicarboxylate cotransporter located in the kidney and small intestine. The secondary structure model of NaDC1 contains 11 transmembrane helices (TM). TM7 was shown previously to contain determinants of citrate affinity, and Arg-349 at the extracellular end of the helix is required for transport. The present study involved cysteine scanning mutagenesis of 26 amino acids in TM7 and the associated loops. All of the mutants were well expressed on the plasma membrane, but many had low or no transport activity: 6 were inactive and 7 had activity less than 25% of the parental. Three of the mutants had notable changes in functional properties. F336C had increased transport activity due to an increased Vmax for succinate. The conserved residue F339C had very low transport activity and a change in substrate selectivity. G356C in the putative extracellular loop was the only cysteine mutant that was affected by the membrane-impermeant cysteine reagent, MTSET. However, direct labeling of G356C with MTSEA-biotin gave a weak signal, indicating that this residue is not readily accessible to more bulky reagents. The results suggest that the amino acids of TM7 are functionally important because their replacement by cysteine had large effects on transport activity. However, most of TM7 does not appear to be accessible to the extracellular fluid and is likely to be an outer helix in contact with the lipid bilayer.
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Affiliation(s)
- Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92093-0718, USA.
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7
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Pajor AM, Sun NN. Single nucleotide polymorphisms in the human Na+-dicarboxylate cotransporter affect transport activity and protein expression. Am J Physiol Renal Physiol 2010; 299:F704-11. [PMID: 20610529 DOI: 10.1152/ajprenal.00213.2010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The sodium-coupled transport of citric acid cycle intermediates in the intestine and kidney is mediated by the Na(+)-dicarboxylate cotransporter, NaDC1. In the kidney, NaDC1 plays an important role in regulating succinate and citrate concentrations in the urine, which may have physiological consequences including the development of kidney stones. In the present study, the impact of nonsynonymous single nucleotide polymorphisms (SNPs) on NaDC1 expression and function was characterized using the COS-7 cell heterologous expression system. The I550V variant had an increased sensitivity to lithium inhibition although there were no significant effects on protein abundance. The L44F variant had no significant effects on expression or function. The membrane protein abundance of the M45L, V117I, and F254L variants was decreased, with corresponding decreases in transport activity. The A310P variant had decreased protein abundance as well as a change in substrate selectivity. The P385S variant had a large decrease in succinate transport V(max), as well as altered substrate selectivity, and a change in the protein glycosylation pattern. The most damaging variant was V477M, which had decreased affinity for both succinate and sodium. The V477M variant also exhibited stimulation by lithium, indicating a change in the high-affinity cation binding site. We conclude that most of the naturally occurring nonsynonymous SNPs affect protein processing of NaDC1, and several also affect functional properties. All of these mutations are predicted to decrease transport activity in vivo, which would result in decreased intestinal and renal absorption of citric acid cycle intermediates.
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Affiliation(s)
- Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Univ. of California, La Jolla, CA 92093-0718, USA.
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8
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Ruiz-Larrañaga O, Garrido JM, Manzano C, Iriondo M, Molina E, Gil A, Koets AP, Rutten VPMG, Juste RA, Estonba A. Identification of single nucleotide polymorphisms in the bovine solute carrier family 11 member 1 (SLC11A1) gene and their association with infection by Mycobacterium avium subspecies paratuberculosis. J Dairy Sci 2010; 93:1713-21. [PMID: 20338449 DOI: 10.3168/jds.2009-2438] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 11/18/2009] [Indexed: 12/23/2022]
Abstract
Johne's disease is a chronic enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP) that causes substantial financial losses for the cattle industry. Susceptibility to MAP infection is reported to be determined in part by genetic factors, so marker-assisted selection could help to obtain bovine populations that are increasingly resistant to MAP infection. Solute carrier family 11 member 1 (SLC11A1) was adjudged to be a potential candidate gene because of its role in innate immunity, its involvement in susceptibility to numerous intracellular infections, and its previous association with bovine MAP infection. The objectives of this study were to carry out an exhaustive process of discovery and compilation of polymorphisms in SLC11A1 gene, and to perform a population-based genetic association study to test its implication in susceptibility to MAP infection in cattle. In all, 57 single nucleotide polymorphisms (SNP) were detected, 25 of which are newly described in Bos taurus. Twenty-four SNP and two 3'-untranslated region polymorphisms, previously analyzed, were selected for a subsequent association study in 558 European Holstein-Friesian animals. The SNP c.1067C>G and c.1157-91A>T and a haplotype formed by these 2 SNP yielded significant association with susceptibility to MAP infection. The c.1067C>G is a nonsynonymous SNP that causes an amino acid change in codon 356 from proline to alanine (P356A) that could alter SLC11A1 protein function. This association study supports the involvement of SLC11A1 gene in susceptibility to MAP infection in cattle. Our results suggest that SNP c.1067C>G may be a potential causal variant, although functional studies are needed to assure this point.
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Affiliation(s)
- O Ruiz-Larrañaga
- Genetics, Physical Anthropology, and Animal Physiology Department, University of the Basque Country, Sarriena s/n, 48940 Leioa, Bizkaia, Spain
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9
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Thomas R, Vostrikov VV, Greathouse DV, Koeppe RE. Influence of proline upon the folding and geometry of the WALP19 transmembrane peptide. Biochemistry 2010; 48:11883-91. [PMID: 19891499 DOI: 10.1021/bi9016395] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The orientations, geometries, and lipid interactions of designed transmembrane (TM) peptides have attracted significant experimental and theoretical interest. Because the amino acid proline will introduce a known discontinuity into an alpha helix, we have sought to measure the extent of helix kinking caused by a single proline within the isolated TM helical domain of WALP19. For this purpose, we synthesized acetyl-GWWLALALAP(10)ALALALWWA-ethanolamide and included pairs of deuterated alanines by using 60-100% Fmoc-l-Ala-d(4) at selected sequence positions. Solid-state deuterium ((2)H) magnetic resonance spectra from oriented, hydrated samples (1/40, peptide/lipid; using several lipids) reveal signals from many of the alanine backbone C(alpha) deuterons as well as the alanine side-chain C(beta) methyl groups, whereas signals from C(alpha) deuterons generally have not been observed for similar peptides without proline. It is conceivable that altered peptide dynamics may be responsible for the apparent "unmasking" of the backbone resonances in the presence of the proline. Data analysis using the geometric analysis of labeled alanines (GALA) method reveals that the peptide helix is distorted due to the presence of the proline. To provide additional data points for evaluating the segmental tilt angles of the two halves of the peptide, we substituted selected leucines with l-Ala-d(4). Using this approach, we were able to deduce that the apparent average tilt of the C-terminal increases from approximately 4 degrees to approximately 12 degrees when Pro(10) is introduced. The segment N-terminal to proline is more complex and possibly is more dynamically flexible; Leu to Ala mutations within the N-terminal segment alter the average orientations of alanines in both segments. Nevertheless, in DOPC, we could estimate an apparent kink angle of approximately 19 degrees . Together, the results suggest that the central proline influences not only the geometry but also the dynamics of the membrane-spanning peptide. The results make up an important basis for understanding the functional role of proline in several families of membrane proteins.
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Affiliation(s)
- Rachel Thomas
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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10
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Hussainzada N, Claro Da Silva T, Swaan PW. The cytosolic half of helix III forms the substrate exit route during permeation events of the sodium/bile acid cotransporter ASBT. Biochemistry 2009; 48:8528-39. [PMID: 19653651 DOI: 10.1021/bi900616w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed alkylation of consecutively introduced cysteines was employed to probe the solvent-accessible profile of highly conserved transmembrane helix 3 (TM3), spanning residues V127-T149 of the apical sodium-dependent bile acid transporter (ASBT), a key membrane protein involved in cholesterol homeostasis. Sequence alignment of SLC10 family members has previously identified a signature motif (ALGMMPL) localized to TM3 of ASBT with as yet undetermined function. Cysteine mutagenesis of this motif resulted in severe decreases in uptake activity only for mutants M141C and P142C. Additional conservative and nonconservative replacement of P142 suggests its structural and functional importance during the ASBT transport cycle. Significant decreases in transport activity were also observed for three cysteine mutants clustered along the exofacial half of the helix (M129C, T130C, S133C) and five mutants consecutively lining the cytosolic half of TM3 (L145C-T149C). Measurable surface expression was detected for all TM3 mutants. Using physicochemically different alkylating reagents, sites predominantly lining the cytosolic half of the TM3 helix were found to be solvent accessible (i.e., S128C, L143C-T149C). Analysis of substrate kinetics for select TM3 mutants demonstrates significant loss of taurocholic acid affinity for mutants S128C and L145C-T149C. Overall, we conclude (i) the functional and structural importance of P142 during the transport cycle and (ii) the presence of a large hydrophilic cleft region lining the cytosolic half of TM3 that may form portions of the substrate exit route during permeation. Our studies provide unique insight into molecular mechanisms guiding the ASBT transport cycle with respect to substrate binding and translocation events.
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Affiliation(s)
- Naissan Hussainzada
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA
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11
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Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins. Biophys J 2008; 95:4384-95. [PMID: 18658225 DOI: 10.1529/biophysj.108.136747] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro50, Pro91, and Pro186 in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro91, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro91 and Pro186 showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.
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12
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Hussainzada N, Khandewal A, Swaan PW. Conformational flexibility of helix VI is essential for substrate permeation of the human apical sodium-dependent bile acid transporter. Mol Pharmacol 2007; 73:305-13. [PMID: 17971420 DOI: 10.1124/mol.107.041640] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The present study characterizes the methanethiosulfonate (MTS) inhibition profiles of 26 consecutive cysteine-substituted mutants comprising transmembrane (TM) helix 6 of the human apical Na(+)-dependent bile acid transporter (SLC10A2). TM6 is linked exofacially to TM7 via extracellular loop 3. TM7 was identified previously as lining part of the substrate permeation path ( Mol Pharmacol 70: 1565, 2006 ). Most TM6 cysteine replacements were well tolerated, except for five residues with either severely hampered (I229C, G249C) or abolished (P234C, G237C, G241C) activity. Disruption of protein synthesis or folding and stability may account for lack of activity for mutant P234C. Subsequent Pro234 amino acid replacement reveals its participation in both structural and functional aspects of the transport cycle. Application of polar MTS reagents (1 mM) significantly inhibited the activity of six mutants (V235C, S239C, F242C, R246C, A248C, and Y253C), for which rates of modification were almost fully reversed (except Y253C) upon inclusion of bile acid substrates or removal of Na(+) from the MTS preincubation medium. Activity assessments at equilibrative [Na(+)] revealed numerous Na(+)-sensitive residues, suggesting their proximity in or around Na(+) interaction sites. In silico modeling reveals the intimate and potentially cooperative orientation of MTS-accessible TM6 residues toward functionally important TM7 amino acids, substantiating TM6 participation during the transport cycle. We conclude a functional requirement for helical flexibility imparted by Pro234, Gly237, and Gly241, probably forming a "conformational switch" requisite for substrate turnover; meanwhile, MTS-accessible residues, which line a helical face spatially distinct from this switch, may participate during substrate permeation.
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Affiliation(s)
- Naissan Hussainzada
- Department of Pharmaceutical Sciences, University of Maryland, 621 HSF-II, 20 Penn Street, Baltimore, MD 21201, USA
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13
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Weerachayaphorn J, Pajor AM. Sodium-dependent extracellular accessibility of Lys-84 in the sodium/dicarboxylate cotransporter. J Biol Chem 2007; 282:20213-20. [PMID: 17504760 PMCID: PMC2864014 DOI: 10.1074/jbc.m701113200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Na(+)/dicarboxylate cotransporter transports Na(+) with citric acid cycle intermediates such as succinate and citrate. The present study focuses on transmembrane helix 3, which is highly conserved among the members of the SLC13 family. Fifteen amino acids in the extracellular half of transmembrane helix (amino acids 98-112) as well as Lys-84, previously shown to affect substrate affinity, were mutated individually to cysteine and expressed in the human retinal pigment epithelial cell line. Transport specificity ratio analysis shows that determinants for distinguishing succinate and citrate are found at amino acids Lys-84, Glu-101, Trp-103, His-106, and Leu-111. All of the mutants were tested for sensitivity to the membrane-impermeant cysteine-specific reagent (2-sulfonatoethyl) methanethiosulfonate (MTSES), but only K84C was sensitive to MTSES inhibition. The sensitivity of K84C to MTSES was greatest in the presence of sodium, and the inhibition could be prevented by addition of substrate or replacement of sodium, indicating that the accessibility of Lys-84 changes with conformational state. The substrate protection of MTSES inhibition of K84C appears to occur early in the transport cycle, before the large-scale conformational change associated with translocation of substrate. The results point to a new location for Lys-84 within the substrate access pore of the Na(+)/dicarboxylate cotransporter, either in a transmembrane helix or a reentrant loop facing a water-filled pore.
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Affiliation(s)
- Jittima Weerachayaphorn
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0645, USA
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