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Bahia MS, Khazanov N, Zhou Q, Yang Z, Wang C, Hong JS, Rab A, Sorscher EJ, Brouillette CG, Hunt JF, Senderowitz H. Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator. J Chem Inf Model 2021; 61:1762-1777. [PMID: 33720715 DOI: 10.1021/acs.jcim.0c01207] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cystic Fibrosis (CF) is caused by mutations to the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel. CFTR is composed of two membrane spanning domains, two cytosolic nucleotide-binding domains (NBD1 and NBD2) and a largely unstructured R-domain. Multiple CF-causing mutations reside in the NBDs and some are known to compromise the stability of these domains. The ability to predict the effect of mutations on the stability of the cytosolic domains of CFTR and to shed light on the mechanisms by which they exert their effect is therefore important in CF research. With this in mind, we have predicted the effect on domain stability of 59 mutations in NBD1 and NBD2 using 15 different algorithms and evaluated their performances via comparison to experimental data using several metrics including the correct classification rate (CCR), and the squared Pearson correlation (R2) and Spearman's correlation (ρ) calculated between the experimental ΔTm values and the computationally predicted ΔΔG values. Overall, the best results were obtained with FoldX and Rosetta. For NBD1 (35 mutations), FoldX provided R2 and ρ values of 0.64 and -0.71, respectively, with an 86% correct classification rate (CCR). For NBD2 (24 mutations), FoldX R2, ρ, and CCR were 0.51, -0.73, and 75%, respectively. Application of the Rosetta high-resolution protocol (Rosetta_hrp) to NBD1 yielded R2, ρ, and CCR of 0.64, -0.75, and 69%, respectively, and for NBD2 yielded R2, ρ, and CCR of 0.29, -0.27, and 50%, respectively. The corresponding numbers for the Rosetta's low-resolution protocol (Rosetta_lrp) were R2 = 0.47, ρ = -0.69, and CCR = 69% for NBD1 and R2 = 0.27, ρ = -0.24, and CCR = 63% for NBD2. For NBD1, both algorithms suggest that destabilizing mutations suffer from destabilizing vdW clashes, whereas stabilizing mutations benefit from favorable H-bond interactions. Two triple consensus approaches based on FoldX, Rosetta_lpr, and Rosetta_hpr were attempted using either "majority-voting" or "all-voting". The all-voting consensus outperformed the individual predictors, albeit on a smaller data set. In summary, our results suggest that the effect of mutations on the stability of CFTR's NBDs could be largely predicted. Since NBDs are common to all ABC transporters, these results may find use in predicting the effect and mechanism of the action of multiple disease-causing mutations in other proteins.
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Affiliation(s)
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Qingxian Zhou
- School of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Zhengrong Yang
- School of Medicine, Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Chi Wang
- 702 Fairchild Center, MC3423, Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Jeong S Hong
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Andras Rab
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Eric J Sorscher
- Department of Paediatrics, Emory University School of Medicine, Atlanta, Georgia 30303, United States
| | - Christie G Brouillette
- Department of Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - John F Hunt
- 702 Fairchild Center, MC3423, Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, Hunt JF. Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator. J Biol Chem 2018; 293:17685-17704. [PMID: 29903914 PMCID: PMC6240863 DOI: 10.1074/jbc.ra117.000819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/31/2018] [Indexed: 01/07/2023] Open
Abstract
Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.
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Affiliation(s)
- Chi Wang
- From the Departments of Biological Sciences and
| | - Andrei A. Aleksandrov
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Zhengrong Yang
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | | | - Elizabeth A. Proctor
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pradeep Kota
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jianli An
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | - Anna Kaplan
- From the Departments of Biological Sciences and
| | - Netaly Khazanov
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Brent R. Stockwell
- From the Departments of Biological Sciences and ,Chemistry, Columbia University, New York, New York 10027
| | - Hanoch Senderowitz
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Nikolay V. Dokholyan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R. Riordan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - John F. Hunt
- From the Departments of Biological Sciences and , To whom correspondence should be addressed. Tel.:
212-854-5443; Fax:
212-865-8246; E-mail:
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Yang Z, Hildebrandt E, Jiang F, Aleksandrov AA, Khazanov N, Zhou Q, An J, Mezzell AT, Xavier BM, Ding H, Riordan JR, Senderowitz H, Kappes JC, Brouillette CG, Urbatsch IL. Structural stability of purified human CFTR is systematically improved by mutations in nucleotide binding domain 1. Biochim Biophys Acta Biomembr 2018; 1860:1193-1204. [PMID: 29425673 DOI: 10.1016/j.bbamem.2018.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/19/2018] [Accepted: 02/05/2018] [Indexed: 12/17/2022]
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is an ABC transporter containing two transmembrane domains forming a chloride ion channel, and two nucleotide binding domains (NBD1 and NBD2). CFTR has presented a formidable challenge to obtain monodisperse, biophysically stable protein. Here we report a comprehensive study comparing effects of single and multiple NBD1 mutations on stability of both the NBD1 domain alone and on purified full length human CFTR. Single mutations S492P, A534P, I539T acted additively, and when combined with M470V, S495P, and R555K cumulatively yielded an NBD1 with highly improved structural stability. Strategic combinations of these mutations strongly stabilized the domain to attain a calorimetric Tm > 70 °C. Replica exchange molecular dynamics simulations on the most stable 6SS-NBD1 variant implicated fluctuations, electrostatic interactions and side chain packing as potential contributors to improved stability. Progressive stabilization of NBD1 directly correlated with enhanced structural stability of full-length CFTR protein. Thermal unfolding of the stabilized CFTR mutants, monitored by changes in intrinsic fluorescence, demonstrated that Tm could be shifted as high as 67.4 °C in 6SS-CFTR, more than 20 °C higher than wild-type. H1402S, an NBD2 mutation, conferred CFTR with additional thermal stability, possibly by stabilizing an NBD-dimerized conformation. CFTR variants with NBD1-stabilizing mutations were expressed at the cell surface in mammalian cells, exhibited ATPase and channel activity, and retained these functions to higher temperatures. The capability to produce enzymatically active CFTR with improved structural stability amenable to biophysical and structural studies will advance mechanistic investigations and future cystic fibrosis drug development.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA
| | - Fan Jiang
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics and Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Qingxian Zhou
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianli An
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew T Mezzell
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - Bala M Xavier
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA
| | - John R Riordan
- Department of Biochemistry and Biophysics and Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, 701 19th Street South, Birmingham, AL 35294-0007, USA; Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL 35233, USA
| | | | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX 79430, USA.
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Vernon RM, Chong PA, Lin H, Yang Z, Zhou Q, Aleksandrov AA, Dawson JE, Riordan JR, Brouillette CG, Thibodeau PH, Forman-Kay JD. Stabilization of a nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator yields insight into disease-causing mutations. J Biol Chem 2017; 292:14147-14164. [PMID: 28655774 DOI: 10.1074/jbc.m116.772335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 06/16/2017] [Indexed: 11/06/2022] Open
Abstract
Characterization of the second nucleotide-binding domain (NBD2) of the cystic fibrosis transmembrane conductance regulator (CFTR) has lagged behind research into the NBD1 domain, in part because NBD1 contains the F508del mutation, which is the dominant cause of cystic fibrosis. Research on NBD2 has also been hampered by the overall instability of the domain and the difficulty of producing reagents. Nonetheless, multiple disease-causing mutations reside in NBD2, and the domain is critical for CFTR function, because channel gating involves NBD1/NBD2 dimerization, and NBD2 contains the catalytically active ATPase site in CFTR. Recognizing the paucity of structural and biophysical data on NBD2, here we have defined a bioinformatics-based method for manually identifying stabilizing substitutions in NBD2, and we used an iterative process of screening single substitutions against thermal melting points to both produce minimally mutated stable constructs and individually characterize mutations. We present a range of stable constructs with minimal mutations to help inform further research on NBD2. We have used this stabilized background to study the effects of NBD2 mutations identified in cystic fibrosis (CF) patients, demonstrating that mutants such as N1303K and G1349D are characterized by lower stability, as shown previously for some NBD1 mutations, suggesting a potential role for NBD2 instability in the pathology of CF.
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Affiliation(s)
- Robert M Vernon
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - P Andrew Chong
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Hong Lin
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Zhengrong Yang
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Qingxian Zhou
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Jennifer E Dawson
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - John R Riordan
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Christie G Brouillette
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Patrick H Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Julie D Forman-Kay
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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Hudson RP, Dawson JE, Chong PA, Yang Z, Millen L, Thomas PJ, Brouillette CG, Forman-Kay JD. Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface. Mol Pharmacol 2017; 92:124-135. [PMID: 28546419 DOI: 10.1124/mol.117.108373] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanism of action of modulator compounds for the cystic fibrosis transmembrane conductance regulator (CFTR) is key for the optimization of therapeutics as well as obtaining insights into the molecular mechanisms of CFTR function. We demonstrate the direct binding of VX-809 to the first nucleotide-binding domain (NBD1) of human CFTR. Disruption of the interaction between C-terminal helices and the NBD1 core upon VX-809 binding is observed from chemical shift changes in the NMR spectra of residues in the helices and on the surface of β-strands S3, S9, and S10. Binding to VX-809 leads to a significant negative shift in NBD1 thermal melting temperature (Tm), pointing to direct VX-809 interaction shifting the NBD1 conformational equilibrium. An inter-residue correlation analysis of the chemical shift changes provides evidence of allosteric coupling between the direct binding site and the NBD1:CL4 interface, thus enabling effects on the interface in the absence of direct binding in that location. These NMR binding data and the negative Tm shifts are very similar to those previously reported by us for binding of the dual corrector-potentiator CFFT-001 to NBD1 (Hudson et al., 2012), suggesting that the two compounds may share some aspects of their mechanisms of action. Although previous studies have shown an important role for VX-809 in modulating the conformation of the first membrane spanning domain (Aleksandrov et al., 2012; Ren et al., 2013), this additional mode of VX-809 binding provides insight into conformational dynamics and allostery within CFTR.
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Affiliation(s)
- Rhea P Hudson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Jennifer E Dawson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - P Andrew Chong
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Zhengrong Yang
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Linda Millen
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Philip J Thomas
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Christie G Brouillette
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Julie D Forman-Kay
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.).
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Yang Z, Zhou Q, Mok L, Singh A, Swartz DJ, Urbatsch IL, Brouillette CG. Interactions and cooperativity between P-glycoprotein structural domains determined by thermal unfolding provides insights into its solution structure and function. Biochim Biophys Acta Biomembr 2016; 1859:48-60. [PMID: 27783926 DOI: 10.1016/j.bbamem.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/19/2016] [Accepted: 10/21/2016] [Indexed: 12/16/2022]
Abstract
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains. A low calorimetric unfolding enthalpy and minimal structural changes were observed, which are hallmarks of the thermal unfolding of α-helical membrane proteins, because generally only the extramembranous regions undergo significant unfolding. Nucleotide binding increased the unfolding temperature of both transitions to the same extent, suggesting that one nucleotide binding domain (NBD) unfolds with each transition. Combined with the results from the two isolated NBDs, we propose that each DSC transition represents the cooperative unfolding of one NBD and the two contacting intracellular loops. Further, the presence of two transitions in both apo and MgATP bound wild-type Pgp suggests the NBD-dimeric conformation is transient, and that Pgp resides predominantly in the crystallographically observed inward-facing conformation with NBDs separated, even under conditions supporting continuous MgATP hydrolysis. In contrast, DSC of the vanadate-trapped MgADP·Pgp complex and the MgATP-bound catalytically inactive mutant, E552A/E1197A, show an additional transition at much higher temperature, corresponding to the unfolding of the nucleotide-trapped NBD-dimeric outward-facing conformation. The collective results indicate a strong preference for an NBD dissociated, inward-facing conformation of Pgp.
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Affiliation(s)
- Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leo Mok
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Anukriti Singh
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Douglas J Swartz
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA.
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8
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He L, Aleksandrov AA, An J, Cui L, Yang Z, Brouillette CG, Riordan JR. Restoration of NBD1 thermal stability is necessary and sufficient to correct ∆F508 CFTR folding and assembly. J Mol Biol 2014; 427:106-20. [PMID: 25083918 DOI: 10.1016/j.jmb.2014.07.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 11/29/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) (ABCC7), unique among ABC exporters as an ion channel, regulates ion and fluid transport in epithelial tissues. Loss of function due to mutations in the cftr gene causes cystic fibrosis. The most common cystic-fibrosis-causing mutation, the deletion of F508 (ΔF508) from the first nucleotide binding domain (NBD1) of CFTR, results in misfolding of the protein and clearance by cellular quality control systems. The ΔF508 mutation has two major impacts on CFTR: reduced thermal stability of NBD1 and disruption of its interface with membrane-spanning domains (MSDs). It is unknown if these two defects are independent and need to be targeted separately. To address this question, we varied the extent of stabilization of NBD1 using different second-site mutations and NBD1 binding small molecules with or without NBD1/MSD interface mutation. Combinations of different NBD1 changes had additive corrective effects on ∆F508 maturation that correlated with their ability to increase NBD1 thermostability. These effects were much larger than those caused by interface modification alone and accounted for most of the correction achieved by modifying both the domain and the interface. Thus, NBD1 stabilization plays a dominant role in overcoming the ΔF508 defect. Furthermore, the dual target approach resulted in a locked-open ion channel that was constitutively active in the absence of the normally obligatory dependence on phosphorylation by protein kinase A. Thus, simultaneous targeting of both the domain and the interface, as well as being non-essential for correction of biogenesis, may disrupt normal regulation of channel function.
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Affiliation(s)
- Lihua He
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jianli An
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Liying Cui
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - John R Riordan
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Yang Z, Wang C, Zhou Q, An J, Hildebrandt E, Aleksandrov LA, Kappes JC, DeLucas LJ, Riordan JR, Urbatsch IL, Hunt JF, Brouillette CG. Membrane protein stability can be compromised by detergent interactions with the extramembranous soluble domains. Protein Sci 2014; 23:769-89. [PMID: 24652590 PMCID: PMC4093953 DOI: 10.1002/pro.2460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/06/2022]
Abstract
Detergent interaction with extramembranous soluble domains (ESDs) is not commonly considered an important determinant of integral membrane protein (IMP) behavior during purification and crystallization, even though ESDs contribute to the stability of many IMPs. Here we demonstrate that some generally nondenaturing detergents critically destabilize a model ESD, the first nucleotide-binding domain (NBD1) from the human cystic fibrosis transmembrane conductance regulator (CFTR), a model IMP. Notably, the detergents show equivalent trends in their influence on the stability of isolated NBD1 and full-length CFTR. We used differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy to monitor changes in NBD1 stability and secondary structure, respectively, during titration with a series of detergents. Their effective harshness in these assays mirrors that widely accepted for their interaction with IMPs, i.e., anionic > zwitterionic > nonionic. It is noteworthy that including lipids or nonionic detergents is shown to mitigate detergent harshness, as will limiting contact time. We infer three thermodynamic mechanisms from the observed thermal destabilization by monomer or micelle: (i) binding to the unfolded state with no change in the native structure (all detergent classes); (ii) native state binding that alters thermodynamic properties and perhaps conformation (nonionic detergents); and (iii) detergent binding that directly leads to denaturation of the native state (anionic and zwitterionic). These results demonstrate that the accepted model for the harshness of detergents applies to their interaction with an ESD. It is concluded that destabilization of extramembranous soluble domains by specific detergents will influence the stability of some IMPs during purification.
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Affiliation(s)
- Zhengrong Yang
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Chi Wang
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Jianli An
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
| | - Ellen Hildebrandt
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
| | - Luba A Aleksandrov
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - John C Kappes
- Department of Medicine, University of Alabama at BirminghamBirmingham, Alabama
- Birmingham Veterans Affairs Medical Center, Research ServiceBirmingham, Alabama
| | - Lawrence J DeLucas
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
- Department of Optometry, University of Alabama at BirminghamBirmingham, Alabama
| | - John R Riordan
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel HillChapel Hill, North Carolina
- Cystic Fibrosis Treatment and Research Center, The University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, Texas
- Center for Membrane Protein Research, Texas Tech University Health Sciences CenterLubbock, TX
| | - John F Hunt
- Department of Biological Sciences, Columbia UniversityNew York, New York
| | - Christie G Brouillette
- Department of Chemistry, University of Alabama at BirminghamBirmingham, Alabama
- Center for Structural Biology, University of Alabama at BirminghamBirmingham, Alabama
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10
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Hudson RP, Chong PA, Protasevich II, Vernon R, Noy E, Bihler H, An JL, Kalid O, Sela-Culang I, Mense M, Senderowitz H, Brouillette CG, Forman-Kay JD. Conformational changes relevant to channel activity and folding within the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator. J Biol Chem 2012; 287:28480-94. [PMID: 22722932 PMCID: PMC3436552 DOI: 10.1074/jbc.m112.371138] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/08/2012] [Indexed: 11/06/2022] Open
Abstract
Deletion of Phe-508 (F508del) in the first nucleotide binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) leads to defects in folding and channel gating. NMR data on human F508del NBD1 indicate that an H620Q mutant, shown to increase channel open probability, and the dual corrector/potentiator CFFT-001 similarly disrupt interactions between β-strands S3, S9, and S10 and the C-terminal helices H8 and H9, shifting a preexisting conformational equilibrium from helix to coil. CFFT-001 appears to interact with β-strands S3/S9/S10, consistent with docking simulations. Decreases in T(m) from differential scanning calorimetry with H620Q or CFFT-001 suggest direct compound binding to a less thermostable state of NBD1. We hypothesize that, in full-length CFTR, shifting the conformational equilibrium to reduce H8/H9 interactions with the uniquely conserved strands S9/S10 facilitates release of the regulatory region from the NBD dimerization interface to promote dimerization and thereby increase channel open probability. These studies enabled by our NMR assignments for F508del NBD1 provide a window into the conformational fluctuations within CFTR that may regulate function and contribute to folding energetics.
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Affiliation(s)
- Rhea P. Hudson
- From the Molecular Structure and Function Program, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - P. Andrew Chong
- From the Molecular Structure and Function Program, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Irina I. Protasevich
- the Center for Biophysical Science and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400
| | - Robert Vernon
- From the Molecular Structure and Function Program, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Efrat Noy
- the Department of Chemistry, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Hermann Bihler
- the Cystic Fibrosis Foundation Therapeutics, Bedford, Massachusetts 01730
| | - Jian Li An
- the Center for Biophysical Science and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400
| | - Ori Kalid
- Epix Pharmaceuticals, Lexington, Massachusetts 02421-3112
| | | | - Martin Mense
- the Cystic Fibrosis Foundation Therapeutics, Bedford, Massachusetts 01730
| | - Hanoch Senderowitz
- the Department of Chemistry, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Christie G. Brouillette
- the Center for Biophysical Science and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400
- the Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-1240, and
| | - Julie D. Forman-Kay
- From the Molecular Structure and Function Program, Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
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11
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Wang C, Protasevich I, Yang Z, Seehausen D, Skalak T, Zhao X, Atwell S, Spencer Emtage J, Wetmore DR, Brouillette CG, Hunt JF. Integrated biophysical studies implicate partial unfolding of NBD1 of CFTR in the molecular pathogenesis of F508del cystic fibrosis. Protein Sci 2011; 19:1932-47. [PMID: 20687163 DOI: 10.1002/pro.480] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The lethal genetic disease cystic fibrosis is caused predominantly by in-frame deletion of phenylalanine 508 in the cystic fibrosis transmembrane conductance regulator (CFTR). F508 is located in the first nucleotide-binding domain (NBD1) of CFTR, which functions as an ATP-gated chloride channel on the cell surface. The F508del mutation blocks CFTR export to the surface due to aberrant retention in the endoplasmic reticulum. While it was assumed that F508del interferes with NBD1 folding, biophysical studies of purified NBD1 have given conflicting results concerning the mutation's influence on domain folding and stability. We have conducted isothermal (this paper) and thermal (accompanying paper) denaturation studies of human NBD1 using a variety of biophysical techniques, including simultaneous circular dichroism, intrinsic fluorescence, and static light-scattering measurements. These studies show that, in the absence of ATP, NBD1 unfolds via two sequential conformational transitions. The first, which is strongly influenced by F508del, involves partial unfolding and leads to aggregation accompanied by an increase in tryptophan fluorescence. The second, which is not significantly influenced by F508del, involves full unfolding of NBD1. Mg-ATP binding delays the first transition, thereby offsetting the effect of F508del on domain stability. Evidence suggests that the initial partial unfolding transition is partially responsible for the poor in vitro solubility of human NBD1. Second-site mutations that increase the solubility of isolated F508del-NBD1 in vitro and suppress the trafficking defect of intact F508del-CFTR in vivo also stabilize the protein against this transition, supporting the hypothesize that it is responsible for the pathological trafficking of F508del-CFTR.
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Affiliation(s)
- Chi Wang
- Department of Biological Sciences, 702A Fairchild Center, Columbia University, New York, New York 10027, USA
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12
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Protasevich I, Yang Z, Wang C, Atwell S, Zhao X, Emtage S, Wetmore D, Hunt JF, Brouillette CG. Thermal unfolding studies show the disease causing F508del mutation in CFTR thermodynamically destabilizes nucleotide-binding domain 1. Protein Sci 2011; 19:1917-31. [PMID: 20687133 DOI: 10.1002/pro.479] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Misfolding and degradation of CFTR is the cause of disease in patients with the most prevalent CFTR mutation, an in-frame deletion of phenylalanine (F508del), located in the first nucleotide-binding domain of human CFTR (hNBD1). Studies of (F508del)CFTR cellular folding suggest that both intra- and inter-domain folding is impaired. (F508del)CFTR is a temperature-sensitive mutant, that is, lowering growth temperature, improves both export, and plasma membrane residence times. Yet, paradoxically, F508del does not alter the fold of isolated hNBD1 nor did it seem to perturb its unfolding transition in previous isothermal chemical denaturation studies. We therefore studied the in vitro thermal unfolding of matched hNBD1 constructs ±F508del to shed light on the defective folding mechanism and the basis for the thermal instability of (F508del)CFTR. Using primarily differential scanning calorimetry (DSC) and circular dichroism, we show for all hNBD1 pairs studied, that F508del lowers the unfolding transition temperature (T(m)) by 6-7°C and that unfolding occurs via a kinetically-controlled, irreversible transition in isolated monomers. A thermal unfolding mechanism is derived from nonlinear least squares fitting of comprehensive DSC data sets. All data are consistent with a simple three-state thermal unfolding mechanism for hNBD1 ± F508del: N(±MgATP) <==> I(T)(±MgATP) → A(T) → (A(T))(n). The equilibrium unfolding to intermediate, I(T), is followed by the rate-determining, irreversible formation of a partially folded, aggregation-prone, monomeric state, A(T), for which aggregation to (A(T))(n) and further unfolding occur with no detectable heat change. Fitted parameters indicate that F508del thermodynamically destabilizes the native state, N, and accelerates the formation of A(T).
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Affiliation(s)
- Irina Protasevich
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
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13
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Moro WB, Yang Z, Kane TA, Zhou Q, Harville S, Brouillette CG, Brouillette WJ. SAR studies for a new class of antibacterial NAD biosynthesis inhibitors. ACTA ACUST UNITED AC 2010; 11:617-25. [PMID: 19408950 DOI: 10.1021/cc9000357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new lead class of antibacterial drug-like NAD synthetase (NADs) inhibitors was previously identified from a virtual screening study. Here a solution-phase synthetic library of 76 compounds, analogs of the urea-sulfonamide 5838, was synthesized in parallel to explore SAR on the sulfonamide aryl group. All library members were tested for enzyme inhibition against NADs and nicotinic acid mononucleotide adenylyltransferase (NaMNAT), the last two enzymes in the biosynthesis of NAD, and for growth inhibition in a Bacillus anthracis antibacterial assay. Most compounds that inhibited bacterial growth also showed inhibition against one of the enzymes tested. While only modest enhancements in the enzyme inhibition potency against NADs were observed, of significance was the observation that the antibacterial urea-sulfonamides more consistently inhibited NaMNAT.
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Affiliation(s)
- Whitney Beysselance Moro
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
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14
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15
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Atwell S, Brouillette CG, Conners K, Emtage S, Gheyi T, Guggino WB, Hendle J, Hunt JF, Lewis HA, Lu F, Protasevich II, Rodgers LA, Romero R, Wasserman SR, Weber PC, Wetmore D, Zhang FF, Zhao X. Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant. Protein Eng Des Sel 2010; 23:375-84. [PMID: 20150177 DOI: 10.1093/protein/gzq004] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Upon removal of the regulatory insert (RI), the first nucleotide binding domain (NBD1) of human cystic fibrosis transmembrane conductance regulator (CFTR) can be heterologously expressed and purified in a form that remains stable without solubilizing mutations, stabilizing agents or the regulatory extension (RE). This protein, NBD1 387-646(Delta405-436), crystallizes as a homodimer with a head-to-tail association equivalent to the active conformation observed for NBDs from symmetric ATP transporters. The 1.7-A resolution X-ray structure shows how ATP occupies the signature LSGGQ half-site in CFTR NBD1. The DeltaF508 version of this protein also crystallizes as a homodimer and differs from the wild-type structure only in the vicinity of the disease-causing F508 deletion. A slightly longer construct crystallizes as a monomer. Comparisons of the homodimer structure with this and previously published monomeric structures show that the main effect of ATP binding at the signature site is to order the residues immediately preceding the signature sequence, residues 542-547, in a conformation compatible with nucleotide binding. These residues likely interact with a transmembrane domain intracellular loop in the full-length CFTR channel. The experiments described here show that removing the RI from NBD1 converts it into a well-behaved protein amenable to biophysical studies yielding deeper insights into CFTR function.
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Affiliation(s)
- Shane Atwell
- Eli Lilly & Co., 10300 Campus Point Drive, San Diego, CA 92121, USA
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16
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Moro WB, Yang Z, Kane TA, Brouillette CG, Brouillette WJ. Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs). Bioorg Med Chem Lett 2009; 19:2001-5. [PMID: 19249205 DOI: 10.1016/j.bmcl.2009.02.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/05/2009] [Accepted: 02/09/2009] [Indexed: 11/24/2022]
Abstract
Virtual screening was employed to identify new drug-like inhibitors of NAD synthetase (NADs) as antibacterial agents. Four databases of commercially available compounds were docked against three subsites of the NADs active site using FlexX in conjunction with CScore. Over 200 commercial compounds were purchased and evaluated in enzyme inhibition and antibacterial assays. 18 compounds inhibited NADs at or below 100 microM (7.6% hit rate), and two were selected for future SAR studies.
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Affiliation(s)
- Whitney Beysselance Moro
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, United States
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17
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Lu S, Smith CD, Yang Z, Pruett PS, Nagy L, McCombs D, DeLucas LJ, Brouillette WJ, Brouillette CG. Structure of nicotinic acid mononucleotide adenylyltransferase from Bacillus anthracis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:893-8. [PMID: 18931430 PMCID: PMC2564882 DOI: 10.1107/s1744309108029102] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 09/10/2008] [Indexed: 11/10/2022]
Abstract
Nicotinic acid mononucleotide adenylyltransferase (NaMNAT; EC 2.7.7.18) is the penultimate enzyme in the biosynthesis of NAD(+) and catalyzes the adenylation of nicotinic acid mononucleotide (NaMN) by ATP to form nicotinic acid adenine dinucleotide (NaAD). This enzyme is regarded as a suitable candidate for antibacterial drug development; as such, Bacillus anthracis NaMNAT (BA NaMNAT) was heterologously expressed in Escherichia coli for the purpose of inhibitor discovery and crystallography. The crystal structure of BA NaMNAT was determined by molecular replacement, revealing two dimers per asymmetric unit, and was refined to an R factor and R(free) of 0.228 and 0.263, respectively, at 2.3 A resolution. The structure is very similar to that of B. subtilis NaMNAT (BS NaMNAT), which is also a dimer, and another independently solved structure of BA NaMNAT recently released from the PDB along with two ligated forms. Comparison of these and other less related bacterial NaMNAT structures support the presence of considerable conformational heterogeneity and flexibility in three loops surrounding the substrate-binding area.
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Affiliation(s)
- Shanyun Lu
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Craig D. Smith
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
- Department of Vision Sciences, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Zhengrong Yang
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Pamela S. Pruett
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Lisa Nagy
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Deborah McCombs
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Lawrence J. DeLucas
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
- Department of Optometry, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Wayne J. Brouillette
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
| | - Christie G. Brouillette
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
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18
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McDonald HM, Pruett PS, Deivanayagam C, Protasevich II, Carson WM, DeLucas LJ, Brouillette WJ, Brouillette CG. Structural adaptation of an interacting non-native C-terminal helical extension revealed in the crystal structure of NAD+ synthetase from Bacillus anthracis. Acta Crystallogr D Biol Crystallogr 2007; 63:891-905. [PMID: 17642516 DOI: 10.1107/s0907444907029769] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Accepted: 06/18/2007] [Indexed: 11/10/2022]
Abstract
The crystal structures of NH(3)-dependent NAD+ synthetase from Bacillus anthracis as the apoenzyme (1.9 A), in complex with the natural catalytic products AMP and pyrophosphate (2.4 A) and in complex with the substrate analog adenosine 5'-(alpha,beta-methylene)triphosphate (2.0 A) have been determined. NAD+ synthetase catalyzes the last step in the biosynthesis of the vitally important cofactor NAD+. In comparison to other NAD+ synthetase crystal structures, the C-terminal His-tagged end of the apoenzyme adopts a novel helical conformation, causing significant compensatory changes in the region. The structural accommodations observed in B. anthracis NAD+ synthetase are remarkable in the absence of adverse affects on enzyme activity. They also illustrate a rare example of the influence of a non-native C-terminal His-tag extension on the structure of a native protein. In contrast to the apoenzyme, when AMP and pyrophosphate or adenosine 5'-(alpha,beta-methylene)triphosphate are bound, the C-terminus adopts a conformation that allows ATP binding and overall the structure then resembles other NAD+ synthetase structures. The structures of NAD+ synthetase complexes from B. anthracis are compared with published X-ray crystal structures of the enzyme from B. subtilis, Escherichia coli and Helicobacter pylori. These comparisons support the novel observation that P1 and P2 loop ordering is not a consequence of crystal contacts but rather a consequence of intrinsic intramolecular interactions within the ordered subunit.
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Affiliation(s)
- Heather M McDonald
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294-4440, USA
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19
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Velu SE, Mou L, Luan CH, Yang ZW, DeLucas LJ, Brouillette CG, Brouillette WJ. Antibacterial nicotinamide adenine dinucleotide synthetase inhibitors: amide- and ether-linked tethered dimers with alpha-amino acid end groups. J Med Chem 2007; 50:2612-21. [PMID: 17489580 DOI: 10.1021/jm061349l] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tethered dimers incorporating natural alpha-amino acid end groups were synthesized, including examples in which the previously reported esterase-sensitive ester linker was replaced with more stable amide or ether linkers. These compounds remained effective both as inhibitors of NAD synthetase and as potent antibacterial agents for Gram-positive strains. Studies on nonspecific effects, including detergent properties and promiscuous inhibition, suggested little contribution to observed activities.
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Affiliation(s)
- Sadanandan E Velu
- Department of Chemistry, Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, USA
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20
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Brouillette CG, Dong WJ, Yang ZW, Ray MJ, Protasevich II, Cheung HC, Engler JA. Förster resonance energy transfer measurements are consistent with a helical bundle model for lipid-free apolipoprotein A-I. Biochemistry 2006; 44:16413-25. [PMID: 16342934 DOI: 10.1021/bi051018v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apolipoprotein (apo) A-I mutants were constructed for FRET studies to distinguish between two possible lipid-free conformers, a globular helix bundle and an elongated helical hairpin. Mutants containing a single Trp at position 50 were prepared by replacing Trps at positions 8, 72, and 108 with Phe (W@50). Two mutants were constructed from W@50 by incorporating Cys at Arg83 (W@50R83C) or Arg173 (W@50R173C) for attachment of the fluorescent probe AEDANS. Secondary structure of the mutants is very similar to wild type (wt) apo A-I, and fluorescence emission indicates that W50 is protected from solvent. Thermal stabilities of the AEDANS-labeled mutants are also similar to wt. These results indicate that no discernible changes occur in structure or stability as a result of mutations or labeling. The FRET data from W@50 to AEDANS are well-represented by a single distance distribution function with a distance of approximately 22 A for W@50R83C and approximately 19 A for W@50R173C. These distances are consistent with theoretical values calculated from a helical bundle model but not from a helical hairpin. A probability distance distribution function yields significantly small half-width values of 5.6 and 3.7 A, respectively, suggesting low conformational dynamics in both mutants. Differential scanning calorimetry (DSC) was performed on wt and a C-terminal deletion mutant, Delta(187-243), to obtain information on domain architecture. Contrary to expectations, both proteins unfold cooperatively. The results are consistent with the presence of a single folded domain within residues 1-186. These results support the presence of a discrete globular bundle conformation for lipid-free apo A-I.
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Affiliation(s)
- Christie G Brouillette
- Center for Biophysical Sciences and Engineering, Department of Vision Sciences, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.
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21
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Velu SE, Luan CH, Delucas LJ, Brouillette CG, Brouillette WJ. Tethered dimer inhibitors of NAD synthetase: parallel synthesis of an aryl-substituted SAR library. ACTA ACUST UNITED AC 2006; 7:898-904. [PMID: 16283799 DOI: 10.1021/cc050063j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously reported that tethered dimers containing indoles on one end and a permanent positive charge on the other, using a 6-9 carbon polymethylene tether, provided NAD synthetase inhibitors with impressive antibacterial activities against Gram-positives. Here, we report that the phenyl ring is a good substitute for indole, and we utilize solution-phase parallel synthesis to explore structure-activity relationships for substituents on that ring. General conclusions are that nonpolar substituents are more effective than polar ones and that different positional isomers often have very different enzyme inhibition activities. This latter observation reveals that enzyme activity is sensitive to minor structural changes and suggests that nonspecific detergent actions are not important for the observed effects.
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Affiliation(s)
- Sadanandan E Velu
- Department of Chemistry, Department of Vision Sciences, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
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22
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Ren X, Zhao L, Sivashanmugam A, Miao Y, Korando L, Yang Z, Reardon CA, Getz GS, Brouillette CG, Jerome WG, Wang J. Engineering mouse apolipoprotein A-I into a monomeric, active protein useful for structural determination. Biochemistry 2006; 44:14907-19. [PMID: 16274238 DOI: 10.1021/bi0508385] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Apolipoprotein AI (apoAI), the major protein component of HDL, is one of the best predictors of coronary artery disease (CAD), with high apoAI and HDL levels being correlated with low occurrences of CAD. The primary function of apoAI is to recruit phospholipid and cholesterol for assembly of HDL particles. Like other exchangeable apolipoproteins, lipid-free apoAI forms a mixture of different oligomers even at 1.0 mg/mL. This self-association property of the exchangeable apolipoproteins is closely associated with the lipoprotein-binding activity of this protein family. It is unclear if the self-association property of apolipoprotein is required for its lipoprotein-binding activity. We developed a novel method for engineering an oligomeric protein to a monomeric, biologically active protein. Using this method, we generated a monomeric mouse apoAI mutant that is active. This mutant contains the first 216 residues of mouse apoAI and replaces six hydrophobic residues with either polar or smaller hydrophobic residues at the defined positions (V118A/A119S/L121Q/T191S/T195S/T199S). Cross-linking results show that this mutant is greater than 90% monomeric at 8 mg/mL. CD, DSC, and NMR results indicate that the mutant maintains an identical secondary, tertiary structure and stability as those of the wild-type mouse apoAI. Lipid-binding assays suggest that the mutant shares an equal lipoprotein-binding activity as that of the wild-type apoAI. In addition, both the monomeric mutant and the wild-type protein make nearly identical rHDL particles. With this monomeric mouse apoAI, high-quality NMR data has been collected, allowing for the NMR structural determination of lipid-free apoAI. On the basis of these results, we conclude that this apoAI mutant is a monomeric, active apoAI useful for structural determination.
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Affiliation(s)
- Xuefeng Ren
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
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Protasevich II, Brouillette CG, Snow ME, Dunham S, Rubin JR, Gogliotti R, Siegel K. Role of inhibitor aliphatic chain in the thermodynamics of inhibitor binding to Escherichia coli enoyl-ACP reductase and the Phe203Leu mutant: a proposed mechanism for drug resistance. Biochemistry 2004; 43:13380-9. [PMID: 15491144 DOI: 10.1021/bi0492509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The antibacterial target enoyl-acyl carrier protein (ACP) reductase is a homotetrameric enzyme that catalyzes the last reductive step of fatty acid biosynthesis. In the present paper, four 2-(2-hydroxyphenoxy)phenol inhibitors, wherein the 4-position substituent varied from H to n-propyl, were studied to determine the contribution of the aliphatic chain to the binding to the wild-type (wt) enoyl-ACP reductase from Escherichia coli (FabI) and a drug-resistant mutant, (F203L)FabI, in which phenylalanine 203 is mutated to leucine. Thermodynamic parameters of ternary complex formation (enzyme-NAD(+)-inhibitor) were determined by isothermal titration calorimetry. The inhibitor affinity to wt FabI and (F203L)FabI increases with increasing aliphatic chain length, although the corresponding affinity for (F203L)FabI is lower, and also, it shows no detectable binding to the 4-H inhibitor. A distinguishing feature of inhibitor binding to either binary enzyme-NAD(+) complex is the apparent negative cooperativity for binding to the tetramer with half-site occupancy. For both enzymes, binding is enthalpy, DeltaH, driven. However, binding DeltaH becomes less favorable with increasing aliphatic chain length. Increases in affinity are found to be exclusively due to favorable changes in solvation entropy. Incremental changes in thermodynamic parameters within the series of inhibitors binding to wt FabI and (F203L)FabI are approximately the same. However, absolute differences between the two enzymes for binding to a given inhibitor are significant, suggesting different binding modes. This finding, coupled with a binding site conformation that is likely to be more rigid in the mutant, appears to result in the drug resistance of (F203L)FabI.
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Affiliation(s)
- Irina I Protasevich
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, Alabama 35294, USA
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24
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Yang ZW, Tendian SW, Carson WM, Brouillette WJ, Delucas LJ, Brouillette CG. Dimethyl sulfoxide at 2.5% (v/v) alters the structural cooperativity and unfolding mechanism of dimeric bacterial NAD+ synthetase. Protein Sci 2004; 13:830-41. [PMID: 14978314 PMCID: PMC2286739 DOI: 10.1110/ps.03330104] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Dimethyl sulfoxide (DMSO) is commonly used as a cosolvent to improve the aqueous solubility of small organic compounds. Its use in a screen to identify novel inhibitors of the enzyme NAD(+) synthetase led to this investigation of its potential effects on the structure and stability of this 60-kD homodimeric enzyme. Although no effects are observed on the enzyme's catalytic activity, as low as 2.5% (v/v) DMSO led to demonstrable changes in the stability of the dimer and its unfolding mechanism. In the absence of DMSO, the dimer behaves hydrodynamically as a single ideal species, as determined by equilibrium analytical ultracentrifugation, and thermally unfolds according to a two-state dissociative mechanism, based on analysis by differential scanning calorimetry (DSC). In the presence of 2.5% (v/v) DMSO, an equilibrium between the dimer and monomer is now detectable with a measured dimer association constant, K(a), equal to 5.6 x 10(6)/M. DSC curve analysis is consistent with this finding. The data are best fit to a three-state sequential unfolding mechanism, most likely representing folded dimer <==> folded monomer <==> unfolded monomer. The unusually large change in the relative stabilities of dimer and monomer, e.g., the association equilibrium shifts from an infinitely large K(a) down to approximately 10(6)/M, in the presence of relatively low cosolvent concentration is surprising in view of the significant buried surface area at the dimer interface, roughly 20% of the surface area of each monomer is buried. A hypothetical structural mechanism to explain this effect is presented.
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Affiliation(s)
- Zhengrong W Yang
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, 35294-4400, USA
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25
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Chesnokova LS, Slepenkov SV, Protasevich II, Sehorn MG, Brouillette CG, Witt SN. Deletion of DnaK's lid strengthens binding to the nucleotide exchange factor, GrpE: a kinetic and thermodynamic analysis. Biochemistry 2003; 42:9028-40. [PMID: 12885236 DOI: 10.1021/bi0346493] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we have used surface plasmon resonance (SPR) and isothermal microtitration calorimetry (ITC) to study the mechanism of complex formation between the Hsp70 molecular chaperone, DnaK, and its cochaperone, GrpE, which is a nucleotide exchange factor. Experiments were geared toward understanding the influence of DnaK's three domains, the ATPase (residues 1-388), substrate-binding (residues 393-507), and lid (residues 508-638) domains, on complex formation with GrpE. We show that the equilibrium dissociation constants for the interaction of GrpE with wtDnaK, lidless DnaK(2-517), the ATPase domain (2-388), and the substrate-binding fragment (393-507) are 64 (+/-16) nM, 4.0 (+/-1.5) nM, 35 (+/-10) nM, and 67 (+/-11) microM, respectively, and that the on-rate constant for the different reactions varies by over 4 orders of magnitude. SPR experiments revealed that GrpE-DnaK(393-507) complex formation is inhibited by added peptide and abolished when the 33-residue flexible "tail" of GrpE is deleted. Such results strongly suggest that the 33-residue flexible N-terminal tail of GrpE binds in the substrate-binding pocket of DnaK. This unique mode of binding between GrpE's tail and DnaK contributes to, but does not fully explain, the decrease in K(d) from 64 to 4 nM upon deletion of DnaK's lid. The possibility that deletion of DnaK's lid creates a more symmetrically shaped molecule, with enhanced affinity to GrpE, is also discussed. Our results reveal a complex set of molecular interactions between DnaK and its cochaperone GrpE. We discuss the impact of each domain on complex formation and dissociation.
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Affiliation(s)
- Liudmila S Chesnokova
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, Louisiana 71130-3932, USA
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26
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Velu SE, Cristofoli WA, Garcia GJ, Brouillette CG, Pierson MC, Luan CH, DeLucas LJ, Brouillette WJ. Tethered dimers as NAD synthetase inhibitors with antibacterial activity. J Med Chem 2003; 46:3371-81. [PMID: 12852767 DOI: 10.1021/jm030003x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution-phase parallel synthesis of tethered dimers was employed to identify lead inhibitors of bacterial NAD synthetase. Active dimers contained two aromatic end groups joined by a polymethylene linker, with one end group containing a permanent positive charge. Effective inhibitors of NAD synthetase also inhibited the growth of Gram-positive (but not Gram-negative) bacteria, including antibiotic-resistant strains. The desmethyl precursors of active inhibitors lacked a permanent positive charge and were inactive as either enzyme inhibitors or antibacterial agents. Similarly, a close structural analogue of the most active inhibitors contained two additional ether oxygens in the tether and was inactive in both assays. These results are consistent with the premise that NAD synthetase inhibition is responsible for the antibacterial actions and support further studies on NAD synthetase as a new target for antibacterial agents.
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Affiliation(s)
- Sadanandan E Velu
- Center for Biophysical Sciences and Engineering, 1025 18th Street South, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400, USA
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27
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Parker MH, Brouillette CG, Prevelige PE. Kinetic and calorimetric evidence for two distinct scaffolding protein binding populations within the bacteriophage P22 procapsid. Biochemistry 2001; 40:8962-70. [PMID: 11467958 DOI: 10.1021/bi0026167] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A wide variety of viruses require the transient presence of scaffolding proteins to direct capsid assembly. In the case of bacteriophage P22, a model in which the scaffolding protein selectively stabilizes on-pathway growing intermediates has been proposed. The stoichiometry and thermodynamics of binding of the bacteriophage P22 scaffolding protein within the procapsid were analyzed by light scattering and isothermal titration calorimetry. Calorimetric experiments carried out between 10 and 37 degrees C were consistent with the presence of at least two distinct populations of binding sites, in agreement with kinetic evidence obtained by a light scattering assay. Binding to the high-affinity sites occurred at 20 degrees C with a stoichiometry of approximately 60 scaffolding molecules per procapsid and an apparent K(d) of approximately 100-300 nM and was almost completely enthalpy-driven. For the second binding population, precise fitting of the data was impossible due to small heats of binding, but the thermodynamics of binding were clearly distinct from the high-affinity phase. The heat capacity change (DeltaC(p)()) of binding was large for the high-affinity sites and negative for both sets of sites. Addition of sodium chloride (1 M) greatly reduced the magnitude of the apparent DeltaH, in agreement with previous evidence that electrostatic interactions play a major role in binding. A mutant scaffolding protein that forms covalent dimers (R74C/L177I) bound only to the high-affinity sites. These data comprise the first quantitative measurements of the energetics of the coat protein/scaffolding protein interaction.
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Affiliation(s)
- M H Parker
- Laboratory for Biological Calorimetry, Biomolecular Analysis Group, Center for Biophysical Science and Engineering, and Department of Microbiology, University of Alabama at Birmingham, 35294, USA
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28
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Brouillette CG, Anantharamaiah GM, Engler JA, Borhani DW. Structural models of human apolipoprotein A-I: a critical analysis and review. Biochim Biophys Acta 2001; 1531:4-46. [PMID: 11278170 DOI: 10.1016/s1388-1981(01)00081-6] [Citation(s) in RCA: 191] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human apolipoprotein (apo) A-I has been the subject of intense investigation because of its well-documented anti-atherogenic properties. About 70% of the protein found in high density lipoprotein complexes is apo A-I, a molecule that contains a series of highly homologous amphipathic alpha-helices. A number of significant experimental observations have allowed increasing sophisticated structural models for both the lipid-bound and the lipid-free forms of the apo A-I molecule to be tested critically. It seems clear, for example, that interactions between amphipathic domains in apo A-I may be crucial to understanding the dynamic nature of the molecule and the pathways by which the lipid-free molecule binds to lipid, both in a discoidal and a spherical particle. The state of the art of these structural studies is discussed and placed in context with current models and concepts of the physiological role of apo A-I and high-density lipoprotein in atherosclerosis and lipid metabolism.
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Affiliation(s)
- C G Brouillette
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, AL 35294-0005, USA.
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29
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Parker MH, Ortwine DF, O'Brien PM, Lunney EA, Banotai CA, Mueller WT, McConnell P, Brouillette CG. Stereoselective binding of an enantiomeric pair of stromelysin-1 inhibitors caused by conformational entropy factors. Bioorg Med Chem Lett 2000; 10:2427-30. [PMID: 11078193 DOI: 10.1016/s0960-894x(00)00495-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isothermal titration calorimetry was used to analyze the binding of an enantiomeric pair of inhibitors to the stromelysin-1 catalytic domain. Differences in binding affinity are attributable to different conformational entropy penalties suffered upon binding. Two possible explanations for these differences are proposed.
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Affiliation(s)
- M H Parker
- University of Alabama at Birmingham, 35294, USA.
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30
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Zaliauskiene L, Kang S, Brouillette CG, Lebowitz J, Arani RB, Collawn JF. Down-regulation of cell surface receptors is modulated by polar residues within the transmembrane domain. Mol Biol Cell 2000; 11:2643-55. [PMID: 10930460 PMCID: PMC14946 DOI: 10.1091/mbc.11.8.2643] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How recycling receptors are segregated from down-regulated receptors in the endosome is unknown. In previous studies, we demonstrated that substitutions in the transferrin receptor (TR) transmembrane domain (TM) convert the protein from an efficiently recycling receptor to one that is rapidly down regulated. In this study, we demonstrate that the "signal" within the TM necessary and sufficient for down-regulation is Thr(11)Gln(17)Thr(19) (numbering in TM). Transplantation of these polar residues into the wild-type TR promotes receptor down-regulation that can be demonstrated by changes in protein half-life and in receptor recycling. Surprisingly, this modification dramatically increases the TR internalization rate as well ( approximately 79% increase). Sucrose gradient centrifugation and cross-linking studies reveal that propensity of the receptors to self-associate correlates with down-regulation. Interestingly, a number of cell surface proteins that contain TM polar residues are known to be efficiently down-regulated, whereas recycling receptors for low-density lipoprotein and transferrin conspicuously lack these residues. Our data, therefore, suggest a simple model in which specific residues within the TM sequences dramatically influence the fate of membrane proteins after endocytosis, providing an alternative signal for down-regulation of receptor complexes to the well-characterized cytoplasmic tail targeting signals.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Differentiation, B-Lymphocyte/chemistry
- Antigens, Differentiation, B-Lymphocyte/drug effects
- Antigens, Differentiation, B-Lymphocyte/physiology
- Chick Embryo
- Cross-Linking Reagents/pharmacology
- Down-Regulation/drug effects
- Endocytosis/drug effects
- Endocytosis/physiology
- Fibroblasts
- Half-Life
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/drug effects
- Histocompatibility Antigens Class II/physiology
- Lysosomes/drug effects
- Lysosomes/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Protein Structure, Tertiary
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/drug effects
- Receptors, Cell Surface/metabolism
- Receptors, Transferrin/chemistry
- Receptors, Transferrin/drug effects
- Receptors, Transferrin/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/drug effects
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
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Affiliation(s)
- L Zaliauskiene
- Department of Cell Biology, Comprehensive Cancer Center, University of Alabama at Birmingham, 35294-0005, USA
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31
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Borhani DW, Engler JA, Brouillette CG. Human apolipoprotein A-I: structure determination and analysis of unusual diffraction characteristics. Acta Crystallogr D Biol Crystallogr 1999; 55:2013-21. [PMID: 10666577 DOI: 10.1107/s0907444999013128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The crystallization and structure determination of recombinant human apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, is described. The fragment crystallized, residues 44-243 of native apo A-I [apo Delta(1-43)A-I], is very similar to intact native apo A-I in its ability to bind lipid, to be incorporated into high-density lipoproteins and to activate lecithin-cholesterol acyl transferase. Apo Delta(1-43)A-I crystallizes from 1.0-1.4 M sodium citrate pH 6.5-7.5 in space group P2(1)2(1)2(1), with unit-cell parameters a = 97.47, b = 113.87, c = 196.19 A (crystal form I). The crystals exhibit unusual diffraction intensity spikes and axial extinctions that are discussed in the context of the 4 A crystal structure. When flash-cooled to 100 K, the crystals diffract synchrotron radiation to 3 A resolution. Radiation sensitivity and crystal-to-crystal variation have hindered the assembly of a complete 3 A data set.
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Affiliation(s)
- D W Borhani
- Department of Organic Chemistry, Southern Research Institute, Birmingham, AL 35205, USA.
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32
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Parker MH, Lunney EA, Ortwine DF, Pavlovsky AG, Humblet C, Brouillette CG. Analysis of the binding of hydroxamic acid and carboxylic acid inhibitors to the stromelysin-1 (matrix metalloproteinase-3) catalytic domain by isothermal titration calorimetry. Biochemistry 1999; 38:13592-601. [PMID: 10521266 DOI: 10.1021/bi991222g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinases (MMPs) are implicated in diseases such as arthritis and cancer. Among these enzymes, stromelysin-1 can also activate the proenzymes of other MMPs, making it an attractive target for pharmaceutical design. Isothermal titration calorimetry (ITC) was used to analyze the binding of three inhibitors to the stromelysin catalytic domain (SCD). One inhibitor (Galardin) uses a hydroxamic acid group (pK(a) congruent with 8.7) to bind the active site zinc; the others (PD180557 and PD166793) use a carboxylic acid group (pK(a) congruent with 4.7). Binding affinity increased dramatically as the pH was decreased over the range 5.5-7.5. Experiments carried out at pH 6.7 in several different buffers revealed that approximately one and two protons are transferred to the enzyme-inhibitor complexes for the hydroxamic and carboxylic acid inhibitors, respectively. This suggests that both classes of inhibitors bind in the protonated state, and that one amino acid residue of the enzyme also becomes protonated upon binding. Similar experiments carried out with the H224N mutant gave strong evidence that this residue is histidine 224. DeltaG, DeltaH, DeltaS, and DeltaC(p) were determined for the three inhibitors at pH 6.7, and DeltaC(p) was used to obtain estimates of the solvational, translational, and conformational components of the entropy term. The results suggest that: (1) a polar group at the P1 position can contribute a large favorable enthalpy, (2) a hydrophobic group at P2' can contribute a favorable entropy of desolvation, and (3) P1' substituents of certain sizes may trigger an entropically unfavorable conformational change in the enzyme upon binding. These findings illustrate the value of complete thermodynamic profiles generated by ITC in discovering binding interactions that might go undetected when relying on binding affinities alone.
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Affiliation(s)
- M H Parker
- Laboratory for Biological Calorimetry, Biomolecular Analysis Group, Center for Macromolecular Crystallography, University of Alabama at Birmingham 35294, USA
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Borhani DW, Engler JA, Brouillette CG. Crystallization of truncated human apolipoprotein A-I in a novel conformation. Acta Crystallogr D Biol Crystallogr 1999; 55:1578-83. [PMID: 10489452 DOI: 10.1107/s0907444999008914] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The crystallization of recombinant human apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, in a new crystal form is described. The fragment crystallized, residues 44-243 of native apo A-I [apo Delta(1--43)A-I], is very similar to intact native apo A-I in its ability to bind lipid, to be incorporated into high-density lipoproteins and to activate lecithin-cholesterol acyl transferase. Apo Delta(1-43)A-I crystallizes, in the presence of beta-D-octylglucopyranoside, in space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 37. 11, b = 123.62, c = 164.65 A and a diffraction limit of 3.2 A. These form II crystals grow under conditions of significantly lower ionic strength than the original form I crystals (space group P2(1)2(1)2(1), a = 97.47, b = 113.87, c = 196.19 A, diffraction limit 3.0 A). Packing arguments show that the unusual open conformation of apo Delta(1-43)A-I found in the form I crystals cannot be packed into the smaller oddly proportioned form II unit cell. Monomeric apo Delta(1-43)A-I, as either a four-helix bundle ( approximately 75 x 30 x 30 A) or an extended helical rod (approximately 150 x 20 x 20 A), can be packed into the form II unit cell. It is concluded, therefore, that apo Delta(1-43)A-I may have crystallized in one of these distinct conformations in the form II crystals.
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Affiliation(s)
- D W Borhani
- Department of Organic Chemistry, Southern Research Institute, Birmingham, AL 35205, USA.
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Abstract
The two main competing models for the structure of discoidal lipoprotein A-I complexes both presume that the protein component is helical and situated around the perimeter of a lipid bilayer disc. However, the more popular "picket fence" model orients the protein helices perpendicular to the surface of the lipid bilayer, while the alternative "belt" model orients them parallel to the bilayer surface. To distinguish between these models, we have investigated the structure of human lipoprotein A-I using a novel form of polarized internal reflection infrared spectroscopy that can characterize the relative orientation of protein and lipid components in the lipoprotein complexes under native conditions. Our results verify lipid bilayer structure in the complexes and point unambiguously to the belt model.
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Affiliation(s)
- V Koppaka
- Department of Pharmacology, Infectious Diseases Section, and the Johnson Foundation for Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6084, USA
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35
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Rogers DP, Roberts LM, Lebowitz J, Datta G, Anantharamaiah GM, Engler JA, Brouillette CG. The lipid-free structure of apolipoprotein A-I: effects of amino-terminal deletions. Biochemistry 1998; 37:11714-25. [PMID: 9718294 DOI: 10.1021/bi973112k] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Deletion mutants of human apolipoprotein A-I (apo hA-I) have been produced from a bacterial expression system to explore the function of the specific domains comprising residues 1-43, 1-65, 88-98, and 187-243, respectively, in the lipid-free conformation and in the lipid-binding mechanism of apo hA-I. Initial studies on apo Delta(1-43)A-I and apo Delta(187-243)A-I have already been reported. To aid purification of these mutants, a histidine-containing N-terminal extension was incorporated (+his); in cases where comparison with the (-his) construct was possible, little effect on the physical properties due to the (+his) extension was found. All mutants have folded structures in their lipid-free state, however these structures differ widely in their relative thermodynamic stability and extent of secondary structure. The mutant with the fewest residues deleted, apo Delta(88-98)A-I(+his), has the least secondary structure (only 34% helix) and is also the least stable (DeltaG = 2.9 kcal/mol). Determined from sedimentation velocity measurements on the lipid-free proteins, all but apo Delta(1-65)A-I(+his) exhibited a range of conformers in solution, which fluctuated around a highly elongated species (dimensions equal to approximately (14-16) x approximately 2.3 nm). Apo Delta(1-65)A-I(+his) exhibited a discrete species which was less asymmetric (dimensions equal to 9 x 2.9 nm). Apo Delta(88-98)A-I(+his) showed extreme heterogeneity with no predominating conformer. Spectroscopic studies (ANS binding and circular dichroism) indicate that there is little difference in the lipid-free structure of the carboxy-terminal deletion mutant, apo Delta(187-243)A-I(+/-his) compared to wild-type (wt) apo wtA-I(+/-his), but substantial differences are observed between wt and the amino-terminal deletion mutants, apo Delta(1-43)A-I, apo Delta(1-65)A-I(+his), and apo Delta(88-98)A-I(+his). In contrast, the lipid-binding properties are impaired for apo Delta(187-243)A-I(+/-his), as measured by dimyristoyl phosphatidylcholine (DMPC) liposome turbidity clearance kinetics and palmitoyloleoyl phosphatidylcholine (POPC) equilibrium binding. Apo Delta(1-43)A-I, apo Delta(1-65)A-I(+his), and apo Delta(88-98)A-I(+his) show lipid affinities statistically similar to apo wtA-I(+his), but significantly defective DMPC clearance kinetics. Interestingly, lecithin:cholesterol acyltransferase (LCAT) activation results correlate qualitatively with the lipid-binding affinity for all mutants but apo Delta(88-98)A-I(+his), suggesting that this mutant has an altered and possibly noncooperative lipid-bound structure as well as an altered lipid-free structure. These results suggest helix 1 (residues 44-65) and helix 10 (residues 220-240) are both required for native lipid-binding properties, while the presence of internal residues, at least helix 3 (residues 88-98), is essential for proper folding of both the lipid-free and lipid-bound conformations. Importantly, studies on apo Delta(88-98)A-I(+his) provide the first experimental evidence that a native-like structure is not necessary for native-like lipid affinity, but apparently is necessary for both DMPC solubilization and LCAT activation. These results provide support for a hypothetical, multistep structure-based mechanism for apo hA-I lipid binding.
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Affiliation(s)
- D P Rogers
- Department of Biochemistry and Molecular Genetics, Center for Macromolecular Crystallography, University of Alabama at Birmingham Medical Center 35294, USA
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Rogers DP, Roberts LM, Lebowitz J, Engler JA, Brouillette CG. Structural analysis of apolipoprotein A-I: effects of amino- and carboxy-terminal deletions on the lipid-free structure. Biochemistry 1998; 37:945-55. [PMID: 9454585 DOI: 10.1021/bi9713512] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An amino-terminal deletion mutant (residues 1-43) and a carboxy-terminal deletion mutant (residues 187-243) of human apoliprotein A-I (apo hA-I) have been produced from a bacterial expression system to explore the importance of the missing residues for the conformation of apo hA-I. Our focus has been to study the lipid-free structure of apo hA-I to understand how discrete domains influence the conformational plasticity of the protein and, by inference, the mechanism of lipid binding. All spectral and physical measurements indicate that both apo delta(1-43)A-I and apo delta(187-243)A-I have folded, tertiary structures. These structures differ in the specific arrangement of helical domains based, in part, on their relative thermodynamic stability, near- and far-UV CD, limited proteolysis, and the accessibility of tryptophans to fluorescence quenchers. In addition, all data indicate that the folded domains of apo hA-I and apo delta(187-243)A-I are very similar. Results from analytical ultracentrifugation suggest that lipid-free apo hA-I and the deletion mutants each exist in a dynamic equilibrium between a loosely folded, helical bundle and an elongated monomeric helical hairpin. The conformational heterogeneity is consistent with significant ANS binding exhibited by all three proteins and could help to explain the facile lipid binding properties of apo hA-I.
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Affiliation(s)
- D P Rogers
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham Medical Center 35294, USA
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Borhani DW, Rogers DP, Engler JA, Brouillette CG. Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation. Proc Natl Acad Sci U S A 1997; 94:12291-6. [PMID: 9356442 PMCID: PMC24911 DOI: 10.1073/pnas.94.23.12291] [Citation(s) in RCA: 338] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/1997] [Accepted: 08/28/1997] [Indexed: 02/05/2023] Open
Abstract
The structure of truncated human apolipoprotein A-I (apo A-I), the major protein component of high density lipoprotein, has been determined at 4-A resolution. The crystals comprise residues 44-243 (exon 4) of apo A-I, a fragment that binds to lipid similarly to intact apo A-I and that retains the lipid-bound conformation even in the absence of lipid. The molecule consists almost entirely of a pseudo-continuous, amphipathic alpha-helix that is punctuated by kinks at regularly spaced proline residues; it adopts a shape similar to a horseshoe of dimensions 125 x 80 x 40 A. Four molecules in the asymmetric unit associate via their hydrophobic faces to form an antiparallel four-helix bundle with an elliptical ring shape. Based on this structure, we propose a model for the structure of apo A-I bound to high density lipoprotein.
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Affiliation(s)
- D W Borhani
- Department of Organic Chemistry, Southern Research Institute, Birmingham, AL 35205, USA.
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Roberts LM, Ray MJ, Shih TW, Hayden E, Reader MM, Brouillette CG. Structural analysis of apolipoprotein A-I: limited proteolysis of methionine-reduced and -oxidized lipid-free and lipid-bound human apo A-I. Biochemistry 1997; 36:7615-24. [PMID: 9200714 DOI: 10.1021/bi962952g] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The domain structures of lipid-free and lipid-bound apolipoprotein A-I (apo A-I) containing reduced and oxidized methionines were analyzed by limited proteolysis. Lipid-free apo A-I is cleaved primarily in the extreme carboxy-terminus and, to a much lesser extent, in the central region of the protein between residues 115 and 136. Oxidation of methionines 112 and 148 to the corresponding sulfoxides in putative amphipathic helices 4 (P99-E120) and 6 (P143-A164), respectively, causes helices 1 (L44-G65), 2 (P66-S87), and 7 (P165-G186) to become susceptible to protease digestion. These results are consistent with a discrete, globular tertiary structure for the lipid-free protein minimally formed from amphipathic helices 1, 2, 4, 6, and 7. In distinct contrast to lipid-free apo A-I, lipid-bound apo A-I is most susceptible to cleavage in the extreme amino-terminus and, to a lesser extent, in both the central and carboxy-terminal regions. The observed cleavage pattern for the reduced lipid-bound protein supports the existence of many of the turns between helices predicted by sequence analysis of the lipid-bound protein. Methionine oxidation of lipid-bound protein results in a decreased protease susceptibility in the extreme amino-terminus and a concomitant increase in protease susceptibility in the central and carboxy-terminal regions. The results from methionine oxidation indicate the oxidation state of the protein is an important determinant in defining the conformation of both lipid-free and lipid-bound apo A-I.
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Affiliation(s)
- L M Roberts
- Department of Biological Chemistry, Southern Research Institute, Birmingham, Alabama 35255-5305, USA
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Rogers DP, Brouillette CG, Engler JA, Tendian SW, Roberts L, Mishra VK, Anantharamaiah GM, Lund-Katz S, Phillips MC, Ray MJ. Truncation of the amino terminus of human apolipoprotein A-I substantially alters only the lipid-free conformation. Biochemistry 1997; 36:288-300. [PMID: 9003180 DOI: 10.1021/bi961876e] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An amino-terminal deletion mutant (residues 1-43) of human apolipoprotein A-I (apo hA-I) has been produced from a bacterial expression system to explore the structural and functional role of these amino acids, encoded by exon 3, in apo hA-I. Lipid binding of apo delta (1-43)A-I and lipid binding of apo hA-I are very similar as assessed by surface activity, lipid association with palmitoyloleoylphosphatidylcholine (POPC) vesicles, and lipid association with plasma lipoproteins. Preliminary kinetic measurements appear to show that the reactivity of lecithin:cholesterol acyltransferase (LCAT) with the mutant is slightly decreased compared to wild-type apo hA-I. Collectively, these results indicate that the N-terminal region is not necessary for lipid binding or activation of LCAT. In contrast, there are significant structural differences between lipid-free apo delta (1-43)A-I and apo hA-I, as judged by denaturant-induced unfolding, binding of the fluorescent probe 1-anilinonaphthalene-8-sulfonate, surface balance measurements, and far- and near-ultraviolet circular dichroic spectroscopy. All spectral and physical measurements indicate apo delta (1-43)A-I has a folded, tertiary structure, although it is significantly less stable than that of apo hA-I. It is concluded that the N-terminal 43 residues are an important structural element of the lipid-free conformational state of apo hA-I, the absence of which induces a fundamentally different fold for the remaining carboxy-terminal residues, compared to those in native apo hA-I.
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Affiliation(s)
- D P Rogers
- Biochemistry Department, Southern Research Institute, Birmingham, Alabama 35209, USA
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Wu H, Myszka DG, Tendian SW, Brouillette CG, Sweet RW, Chaiken IM, Hendrickson WA. Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding. Proc Natl Acad Sci U S A 1996; 93:15030-5. [PMID: 8986758 PMCID: PMC26350 DOI: 10.1073/pnas.93.26.15030] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The T-cell antigen coreceptor CD4 also serves as the receptor for the envelope glycoprotein gp120 of HIV. Extensive mutational analysis of CD4 has implicated residues from a portion of the extracellular amino-terminal domain (D1) in gp120 binding. However, none of these proteins has been fully characterized biophysically, and thus the precise effects on molecular structure and binding interactions are unknown. In the present study, we produced soluble versions of three mutant CD4 molecules (F43V, G47S, and A55F) and characterized their structural properties, thermostability, and ability to bind gp120. Crystallographic and thermodynamic analysis showed minimal structural alterations in the F43V and G47S mutant proteins, which have solvent-exposed mutant side chains. In contrast, some degree of disorder appears to exist in the folded state of A55F, as a result of mutating a buried side chain. Real time kinetic measurements of the interaction of the mutant proteins with gp120 showed affinity decreases of 5-fold for G47S, 50-fold for A55F, and 200-fold for F43V. Although both rate constants for the binding reaction were affected by these mutations, the loss in affinity was mainly due to a decrease in on rates, with less drastic changes occurring in the off rates. These observations suggest the involvement of conformational adaptation in the CD4-gp120 interaction. Together, the structural and kinetic data confirm that F43V is a critical residue in gp120 recognition site, which may also include main chain interactions at residue Gly-47.
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Affiliation(s)
- H Wu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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Tendian SW, Myszka DG, Sweet RW, Chaiken IM, Brouillette CG. Interdomain communication of T-cell CD4 studied by absorbance and fluorescence difference spectroscopy measurements of urea-induced unfolding. Biochemistry 1995; 34:6464-74. [PMID: 7756278 DOI: 10.1021/bi00019a028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
CD4 is a transmembrane glycoprotein expressed on T-lymphocytes. It is a receptor for class II major histocompatibility complex (MHC) molecules and for the HIV envelope glycoprotein gp120. The extracellular portion of CD4 (sCD4) is a rod-shaped molecule consisting of four domains designated D1 through D4. Denaturant-induced unfolding of sCD4 and of isolated CD4 domains, D1D2 and D3D4, was measured using both ultraviolet absorbance and fluorescence difference spectroscopy. Though both absorbance and fluorescence changes arise from changes in the solvent exposure of the intrinsic tryptophan chromophores, the unfolding curves obtained with the two techniques looked very different for sCD4 and D3D4. This dissimilarity is indicative of a greater than two-state unfolding mechanism. The global three-state fit for sCD4, which simultaneously fit both absorbance and emission data to a model with one thermodynamically stable unfolding intermediate, was significantly better than the best two-state fit, suggesting that there are two unfolding regions. Unfolding of isolated D3D4 also fit a three-state model while unfolding of isolated D1D2 fit satisfactorily to a two-state model. The unfolding of these two isolated fragments could not be summed to yield the unfolding profile of sCD4, implying that an interaction between D2 and D3 is lost by splitting sCD4 between these domains. The unfolding data of isolated D1D2 and D3D4 were used with the solvent-accessible surface area of tryptophans calculated from atomic crystal structure coordinates of human D1D2 and rat D3D4 to assign the unfolding steps. The data are consistent with a model for sCD4 unfolding wherein the one stable intermediate appears to contain only the D4 domain unfolded. The remaining three domains apparently unfold as a unit. Furthermore, interactions between domains D1, D2, and D3 appear to stabilize D4, suggesting that stabilizing interactions exist between D3 and D4 even though the unfolding of the D3D4 fragment is best fit by a three-state model. This report is the first to describe a thermodynamic basis for a wide range of biological properties implicated for CD4.
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Affiliation(s)
- S W Tendian
- Southern Research Institute, Birmingham, Alabama 35205, USA
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43
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Segrest JP, Garber DW, Brouillette CG, Harvey SC, Anantharamaiah GM. The amphipathic alpha helix: a multifunctional structural motif in plasma apolipoproteins. Adv Protein Chem 1994; 45:303-69. [PMID: 8154372 DOI: 10.1016/s0065-3233(08)60643-9] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- J P Segrest
- Department of Medicine, University of Alabama 35294
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Kappes JC, Parkin JS, Conway JA, Kim J, Brouillette CG, Shaw GM, Hahn BH. Intracellular transport and virion incorporation of vpx requires interaction with other virus type-specific components. Virology 1993; 193:222-33. [PMID: 8438567 DOI: 10.1006/viro.1993.1118] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Viral protein X (vpx) is a virion-associated HIV-2/SIV accessory protein that enhances viral infectivity and replication in natural target cells. To investigate whether other viral components affect its biosynthesis, subcellular localization, and virion incorporation, we expressed HIV-2 vpx in a mammalian cell system and examined its transport and packaging requirements using an in trans complementation assay. The complete vpx coding region of HIV-2ST was placed under the control of a high-efficiency promoter system (SR alpha) which contained both an SV40 promoter/enhancer region and R/U5 elements of the HTLV-1 LTR. Following transfection of Cos-1 cells, this construct (pSR alpha-vpx) facilitated high level expression of vpx, as demonstrated by Western blot analysis of transfected cell lysates. Moreover, indirect immunofluorescence analysis revealed an intense vpx staining pattern distributed evenly throughout the cytoplasm of transfected cells. This distribution differed markedly from cells expressing wild-type HIV-2 in which vpx localized to the inner surface of the plasma membrane. To determine whether other HIV components were required for this surface localization, we expressed vpx in the context of replication competent HIV-1 and HIV-2 proviruses. Following cotransfection with a vpx-deficient HIV-2 provirus (pXM7), eukaryotically expressed vpx targeted to the plasma membrane and colocalized with HIV-2 p27 gag in a pattern indistinguishable from wild-type HIV-2. Moreover, progeny virions from cotransfected Cos-1 cells contained wild-type amounts of vpx protein, demonstrating that vpx could be efficiently packaged in trans. Under the same experimental conditions, cotransfection of vpx with wild-type HIV-1 (pHXB2) and with vpr-deficient HIV-1 (pR2) failed to result in detectable cell surface targeting or virion incorporation of vpx despite its high level cellular expression. These results demonstrate that efficient intracellular transport and packaging of vpx require interaction with other type-specific virus components.
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Affiliation(s)
- J C Kappes
- Department of Medicine, University of Alabama, Birmingham 35294
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45
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Muccio DD, Waterhous DV, Fish F, Brouillette CG. Analysis of the two-state behavior of the thermal unfolding serum retinol binding protein containing a single retinol ligand. Biochemistry 1992; 31:5560-7. [PMID: 1610801 DOI: 10.1021/bi00139a019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Through the use of CD and DSC, the thermal unfolding of holo serum retinol binding protein containing a single, tightly bound retinol ligand was studied at pH 7.4. The DSC endotherm of the holoprotein ([retinol]/[protein] = 1) was asymmetric about the transition temperature of 78 degrees C. Using changes in ellipticity at 230 nm, the thermal unfolding curve was also asymmetric about the inflection point centered near 78 degrees C. van't Hoff enthalpies were determined by three means and compared to the calorimetric enthalpy (delta Hcal) of 200 kcal/mol. A van't Hoff enthalpy of 190 kcal/mol was determined from the dependence of transition temperature on the concentration of the ligand-bound protein. This value agreed well with the van't Hoff enthalpies found from fits of the DSC (delta HvH = 184 kcal/mol) and spectroscopic (delta HvH = 181 kcal/mol) curves to a two-state thermodynamic model that included ligand dissociation (NR in equilibrium with U+R, where NR is the native holoprotein, U is the unfolded apoprotein, and R is retinol). Poor agreement was obtained with a two-state model that ignored ligand dissociation (N in equilibrium with U). Furthermore, the NR in equilibrium with U+R model accounted for the asymmetry in both CD and DSC transitions and yielded a much improved fit of the data over the N in equilibrium with U model. From these considerations and simulations on other equilibrium models, it is suggested that the NR in equilibrium with U+R model is the simplest model that describes the thermal unfolding of this ligand-bound protein.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D D Muccio
- Department of Chemistry, University of Alabama, Birmingham 35294
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46
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Segrest JP, Jones MK, De Loof H, Brouillette CG, Venkatachalapathi YV, Anantharamaiah GM. The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function. J Lipid Res 1992. [DOI: 10.1016/s0022-2275(20)41536-6] [Citation(s) in RCA: 702] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Segrest JP, Jones MK, De Loof H, Brouillette CG, Venkatachalapathi YV, Anantharamaiah GM. The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function. J Lipid Res 1992; 33:141-66. [PMID: 1569369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Site-directed mutagenesis and other molecular biology-based techniques are now available for probing the amphipathic alpha helix structural motif in the exchangeable apolipoproteins. Here we survey the published literature on lipid-binding and functional domains in apolipoproteins A-I, A-II, A-IV, C-I, C-II, C-III, and E and compare these results with recently developed computer methods for analysis of the location and properties of amphipathic helixes. This comparison suggests that there are at least three distinct classes of amphipathic helixes (classes A, Y, and G*) in the exchangeable apolipoproteins whose distribution varies within and between the seven apolipoproteins. This comparison further suggests that lipid affinity resides largely in class A amphipathic helixes (Segrest, J. P., et al. 1990. Proteins. 8: 103) and that variations in structure and/or numbers of class A domains in individual apolipoproteins allow a range of lipid affinities from high to low. The positions of the four alpha helixes recently shown to form a 4-helix bundle globular structure in apoE (Wilson, C., et al. 1991. Science. 252: 1817) correspond closely to the four amino-terminal class G* amphipathic helixes of apoE identified by our computer analysis. It is of particular interest, therefore, that all of the exchangeable apolipoproteins except apoA-II and C-I, contain amphipathic helixes of class G*. Additional implications of amphipathic helix heterogeneity for the structure and function of the exchangeable apolipoproteins will be discussed.
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Affiliation(s)
- J P Segrest
- Department of Medicine, UAB Medical Center, Birmingham 35294
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48
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Anantharamaiah GM, Brouillette CG, Engler JA, De Loof H, Venkatachalapathi YV, Boogaerts J, Segrest JP. Role of amphipathic helixes in HDL structure/function. Adv Exp Med Biol 1990; 285:131-40. [PMID: 1907078 DOI: 10.1007/978-1-4684-5904-3_17] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In a recent analysis we classified amphipathic helix domains into a minimum of seven distinct classes. Four amphipathic helix classes are found in lipid-associating proteins: apolipoproteins, certain polypeptide hormones, polypeptide venoms and antibiotics, and certain complex transmembrane proteins. Three amphipathic helix classes are involved in both intra- and intermolecular protein-protein interactions: calmodulin-regulated protein kinases, coiled-coil containing proteins that include the so-called leucine zipper, and globular helical proteins. Three central hypothesis have been developed in our studies of the apolipoprotein class of amphipathic helixes: 1) The "Snorkel" hypothesis proposes that when the amphipathic helix is associated with phospholipid, amphipathic basic residues extend toward the polar face of the helix to insert their charged residues into the aqueous milieu: thus the entirety of the uncharged van der Waals' surface of the amphipathic helix is buried within the lipid. 2) We have formulated a hypothesis that Glutamyl residues located at positions 78 and 111 in apolipoprotein A-I on the nonpolar face of two amphipathic helical domains are critical to LCAT activation. 3) The hinged-domain hypothesis was proposed to explain the structural basis for the quantization of HDL subspecies, protein-protein interactions in HDL, and the HDL disc to sphere transformation.
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Anantharamaiah GM, Venkatachalapathi YV, Brouillette CG, Segrest JP. Use of synthetic peptide analogues to localize lecithin:cholesterol acyltransferase activating domain in apolipoprotein A-I. Arteriosclerosis 1990; 10:95-105. [PMID: 2105091 DOI: 10.1161/01.atv.10.1.95] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The major protein of high density lipoprotein (HDL), apolipoprotein (apo) A-I, is the major activator of the plasma enzyme lecithin:cholesterol acyltransferase (LCAT). A consensus amino acid sequence has been defined for the eight, 22-residue long, tandem amphipathic helical repeats located in the carboxy-terminal region of apo A-I. A series of 22 and 44mer synthetic peptide analogues of the consensus domain, differing only in their 13th amino acid residue, were prepared and tested for LCAT activation. One of the peptides was found to equal apo A-I in LCAT activation. This is the first time a peptide activator for LCAT that rivals the activity of apo A-I in the vesicular and discoidal egg phosphatidylcholine assay systems has been synthesized. Based on these results, we propose that the major LCAT-activating domain of apo A-I resides in the 22mer tandem repeats, each containing Glu at the 13th residue and located between residues 66 and 121 in the native apolipoprotein.
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Affiliation(s)
- G M Anantharamaiah
- Department of Medicine, University of Alabama Medical Center, Birmingham 35294
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50
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Affiliation(s)
- J P Segrest
- Department of Medicine, UAB Medical Center, Birmingham, Alabama 35294
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