51
|
Sahu C, Sen K, Pakhira S, Mondal B, Das AK. Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: a theoretical study of enzyme inhibition. J Comput Chem 2013; 34:1907-16. [PMID: 23712937 DOI: 10.1002/jcc.23335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 01/23/2023]
Abstract
The binding properties of a series of benzenesulfonamide inhibitors (4-substituted-ureido-benzenesulfonamides, UBSAs) of human carbonic anhydrase II (hCA II) enzyme with active site residues have been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. To account for the important docking interactions between the UBSAs ligand and hCA II enzyme, a molecular docking program AutoDock Vina is used. The molecular docking results obtained by AutoDock Vina revealed that the docked conformer has root mean square deviation value less than 1.50 Å compared to X-ray crystal structures. The inhibitory activity of UBSA ligands against hCA II is found to be in good agreement with the experimental results. The thermodynamic parameters for inhibitor binding show that hydrogen bonding, hydrophilic, and hydrophobic interactions play a major role in explaining the diverse inhibitory range of these derivatives. Additionally, natural bond orbital analysis is performed to characterize the ligand-metal charge transfer stability. The insights gained from this study have great potential to design new hCA-II inhibitor, 4-[3-(1-p-Tolyl-4-trifluoromethyl-1H-pyrazol-3-yl)-ureido]-benzenesulfonamide, which belongs to the family of UBSA inhibitors and shows similar type of inhibitor potency with hCA II. This work also reveals that a QM/MM model and molecular docking method are computationally feasible and accurate for studying substrate-protein inhibition.
Collapse
Affiliation(s)
- Chandan Sahu
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | | | | | | | | |
Collapse
|
52
|
Zhou L, Li S, Su Y, Yi X, Zheng A, Deng F. Interaction between Histidine and Zn(II) Metal Ions over a Wide pH as Revealed by Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem B 2013; 117:8954-65. [DOI: 10.1021/jp4041937] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lei Zhou
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Shenhui Li
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Yongchao Su
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Xianfeng Yi
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Anmin Zheng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Deng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| |
Collapse
|
53
|
Zhang D, Tugarinov V. Accurate measurements of the effects of deuteration at backbone amide positions on the chemical shifts of ¹⁵N, ¹³Cα, ¹³Cβ, ¹³CO and ¹Hα nuclei in proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 56:169-182. [PMID: 23612994 DOI: 10.1007/s10858-013-9733-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/18/2013] [Indexed: 06/02/2023]
Abstract
An approach towards accurate NMR measurements of deuterium isotope effects on the chemical shifts of all backbone nuclei in proteins ((15)N, (13)Cα, (13)CO, (1)Hα) and (13)Cβ nuclei arising from (1)H-to-D substitutions at amide nitrogen positions is described. Isolation of molecular species with a defined protonation/deuteration pattern at successive backbone nitrogen positions in the polypeptide chain allows quantifying all deuterium isotope shifts of these nuclei from the first to the fourth order. Some of the deuterium isotope shifts measured in the proteins ubiquitin and GB1 can be interpreted in terms of backbone geometry via empirical relationships describing their dependence on (φ; ψ) backbone dihedral angles. Because of their relatively large variability and notable dependence on the protein secondary structure, the two- and three-bond (13)Cα isotope shifts, (2)ΔCα(NiD) and (3)ΔCα(Ni+1D), and three-bond (13)Cβ isotope shifts, (3)ΔCβ(NiD), are useful reporters of the local geometry of the protein backbone.
Collapse
Affiliation(s)
- Daoning Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sci. Bldg./CBSO, College Park, MD 20742, USA
| | | |
Collapse
|
54
|
Fallah-Bagheri A, Moosavi-Movahedi AA, Taghizadeh M, Khodarahmi R, Ma'mani L, Bijari N, Bohlooli M, Shafiee A, Sheibani N, Saboury AA. Modified β-casein restores thermal reversibility of human carbonic anhydrase II: The salt bridge mechanism. Biotechnol Appl Biochem 2013; 60:298-304. [DOI: 10.1002/bab.1081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 12/14/2012] [Indexed: 01/26/2023]
Affiliation(s)
| | | | - Mohammad Taghizadeh
- Institute of Biochemistry and Biophysics; University of Tehran; Tehran; Iran
| | - Reza Khodarahmi
- Medical Biology Research Center; Kermanshah University of Medical Sciences; Kermanshah; Iran
| | - Leila Ma'mani
- Department of Medicinal Chemistry; Faculty of Pharmacy and Pharmaceutical Sciences Research Center; Tehran University of Medical Sciences; Tehran; Iran
| | - Nooshin Bijari
- Medical Biology Research Center; Kermanshah University of Medical Sciences; Kermanshah; Iran
| | - Mousa Bohlooli
- Institute of Biochemistry and Biophysics; University of Tehran; Tehran; Iran
| | | | - Nader Sheibani
- Departments of Ophthalmology and Visual Sciences, and Pharmacology; University of Wisconsin School of Medicine and Public Health; Madison; WI; USA
| | | |
Collapse
|
55
|
Sun H, Long D, Brüschweiler R, Tugarinov V. Carbon Relaxation in 13Cα–Hα and 13Cα–Dα Spin Pairs as a Probe of Backbone Dynamics in Proteins. J Phys Chem B 2013; 117:1308-20. [DOI: 10.1021/jp312292k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hechao Sun
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - Dong Long
- Chemical Sciences Laboratory,
Department of Chemistry and Biochemistry and the National High Magnetic
Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Rafael Brüschweiler
- Chemical Sciences Laboratory,
Department of Chemistry and Biochemistry and the National High Magnetic
Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Vitali Tugarinov
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| |
Collapse
|
56
|
Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Proc Natl Acad Sci U S A 2013; 110:1315-20. [PMID: 23302696 DOI: 10.1073/pnas.1216526110] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The influenza A virus M2 proton channel (A/M2) is the target of the antiviral drugs amantadine and rimantadine, whose use has been discontinued due to widespread drug resistance. Among the handful of drug-resistant mutants, S31N is found in more than 95% of the currently circulating viruses and shows greatly decreased inhibition by amantadine. The discovery of inhibitors of S31N has been hampered by the limited size, polarity, and dynamic nature of its amantadine-binding site. Nevertheless, we have discovered small-molecule drugs that inhibit S31N with potencies greater than amantadine's potency against WT M2. Drug binding locks the protein into a well-defined conformation, and the NMR structure of the complex shows the drug bound in the homotetrameric channel, threaded between the side chains of Asn31. Unrestrained molecular dynamics simulations predicted the same binding site. This S31N inhibitor, like other potent M2 inhibitors, contains a charged ammonium group. The ammonium binds as a hydrate to one of three sites aligned along the central cavity that appear to be hotspots for inhibition. These sites might stabilize hydronium-like species formed as protons diffuse through the outer channel to the proton-shuttling residue His37 near the cytoplasmic end of the channel.
Collapse
|
57
|
Borbat PP, Freed JH. Pulse Dipolar Electron Spin Resonance: Distance Measurements. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
58
|
Fallahbagheri A, Saboury AA, Ma'mani L, Taghizadeh M, Khodarahmi R, Ranjbar S, Bohlooli M, Shafiee A, Foroumadi A, Sheibani N, Moosavi-Movahedi AA. Effects of silica nanoparticle supported ionic liquid as additive on thermal reversibility of human carbonic anhydrase II. Int J Biol Macromol 2012; 51:933-8. [PMID: 22829053 PMCID: PMC3677219 DOI: 10.1016/j.ijbiomac.2012.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/14/2012] [Accepted: 07/16/2012] [Indexed: 12/12/2022]
Abstract
Silica nanoparticle supported imidazolium ionic liquid [SNImIL] was synthesized and utilized as a biocompatible additive for studying the thermal reversibility of human carbonic anhydrase II (HCA II). For this purpose, we prepared additive by modification of nanoparticles through the grafting of ionic liquids on the surface of nanoparticles (SNImIL). The SNImIL were fully characterized by Fourier transform infrared spectroscopy, scanning electron microscopy and thermo gravimetric analysis. The characterization of HCA II was investigated by various techniques including UV-vis and ANS fluorescence spectrophotometry, differential scanning calorimetry, and docking study. SNImIL induced disaggregation, enhanced protein stability and increased thermal reversibility of HCA II by up to 42% at pH 7.75.
Collapse
Affiliation(s)
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Leila Ma'mani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Reza Khodarahmi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Samira Ranjbar
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mousa Bohlooli
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abbas Shafiee
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nader Sheibani
- Departments of Ophthalmology and Visual Sciences and Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ali Akbar Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| |
Collapse
|
59
|
Nyon MP, Kirkpatrick J, Cabrita LD, Christodoulou J, Gooptu B. 1H, 15N and 13C backbone resonance assignments of the archetypal serpin α1-antitrypsin. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:153-156. [PMID: 22109101 PMCID: PMC3438405 DOI: 10.1007/s12104-011-9345-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 11/02/2011] [Indexed: 05/31/2023]
Abstract
Alpha(1)-antitrypsin is a 45-kDa (394-residue) serine protease inhibitor synthesized by hepatocytes, which is released into the circulatory system and protects the lung from the actions of neutrophil elastase via a conformational transition within a dynamic inhibitory mechanism. Relatively common point mutations subvert this transition, causing polymerisation of α(1)-antitrypsin and deficiency of the circulating protein, predisposing carriers to severe lung and liver disease. We have assigned the backbone resonances of α(1)-antitrypsin using multidimensional heteronuclear NMR spectroscopy. These assignments provide the starting point for a detailed solution state characterization of the structural properties of this highly dynamic protein via NMR methods.
Collapse
Affiliation(s)
- Mun Peak Nyon
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| | - John Kirkpatrick
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Lisa D. Cabrita
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - John Christodoulou
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Bibek Gooptu
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| |
Collapse
|
60
|
Rajasekar KV, Campbell LJ, Nietlispach D, Owen D, Mott HR. 1H, 13C and 15N resonance assignments of the GTPase-activating (GAP) and Ral binding domains (GBD) of RLIP76 (RalBP1). BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:119-122. [PMID: 21915608 DOI: 10.1007/s12104-011-9337-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/25/2011] [Indexed: 05/31/2023]
Abstract
RLIP76 (also known as RalBP1) is an effector for Ral small G proteins. RLIP76 is a multifunctional, multi-domain protein that includes a GTPase activating domain for the Rho family (RhoGAP domain) and a GTPase binding domain (GBD) for the Ral small G proteins. The juxtaposition of these two domains (GAP and GBD) may be a strategy employed to co-ordinate regulation of Rho family and Ral-controlled signalling pathways at a crossover node. Here we present the (1)H, (15)N and (13)C NMR backbone and sidechain resonance assignments of the GAP and GBD di-domain (31 kDa).
Collapse
Affiliation(s)
- Karthik V Rajasekar
- Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | | | | | | |
Collapse
|
61
|
Maltsev AS, Ying J, Bax A. Deuterium isotope shifts for backbone ¹H, ¹⁵N and ¹³C nuclei in intrinsically disordered protein α-synuclein. JOURNAL OF BIOMOLECULAR NMR 2012; 54:181-91. [PMID: 22960996 PMCID: PMC3457063 DOI: 10.1007/s10858-012-9666-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 05/09/2023]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise (2)H isotope shift measurements for (13)C(α), (13)C(β), (13)C', (15)N, and (1)H(N) have been obtained by using a mixed sample of protonated and uniformly perdeuterated α-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil (2)H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.
Collapse
Affiliation(s)
- Alexander S Maltsev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
| | | | | |
Collapse
|
62
|
Krejcirikova A, Tugarinov V. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample. JOURNAL OF BIOMOLECULAR NMR 2012; 54:135-43. [PMID: 22960997 DOI: 10.1007/s10858-012-9667-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 08/29/2012] [Indexed: 05/20/2023]
Abstract
The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-(2)H,(15)N,(13)C; Ileδ1-{(13)CH(3)}; Leu,Val-{(13)CH(3)/(12)CD(3)}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-ΔYRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 °C to improve the sensitivity of the measurements and alleviate the overlap of (1)H-(15)N correlations in the abundant α-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of (1)H-(15)N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D (1)H-(15)N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.
Collapse
Affiliation(s)
- Anna Krejcirikova
- Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sci. Bldg./CBSO, College Park, MD 20742, USA
| | | |
Collapse
|
63
|
Iordanov I, Renault M, Réat V, Bosshart PD, Engel A, Saurel O, Milon A. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2344-53. [DOI: 10.1016/j.bbamem.2012.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
|
64
|
Sun H, Tugarinov V. Precision Measurements of Deuterium Isotope Effects on the Chemical Shifts of Backbone Nuclei in Proteins: Correlations with Secondary Structure. J Phys Chem B 2012; 116:7436-48. [DOI: 10.1021/jp304300n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hechao Sun
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Vitali Tugarinov
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
65
|
Ranjbar S, Ghobadi S, Khodarahmi R, Nemati H. Spectroscopic characterization of furosemide binding to human carbonic anhydrase II. Int J Biol Macromol 2012; 50:910-7. [PMID: 22343084 DOI: 10.1016/j.ijbiomac.2012.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/07/2012] [Accepted: 02/07/2012] [Indexed: 11/17/2022]
Abstract
This study reports the interaction between furosemide and human carbonic anhydrase II (hCA II) using fluorescence, UV-vis and circular dichroism (CD) spectroscopy. Fluorescence data indicated that furosemide quenches the intrinsic fluorescence of the enzyme via a static mechanism and hydrogen bonding and van der Walls interactions play the major role in the drug binding. The binding average distance between furosemide and hCA II was estimated on the basis of the theory of Förster energy transfer. Decrease of protein surface hydrophobicity was also documented upon furosemide binding. Chemical modification of hCA II using N-bromosuccinimide indicated decrease of the number of accessible tryptophans in the presence of furosemide. CD results suggested the occurance of some alterations in α-helical content as well as tertiary structure of hCA II upon drug binding.
Collapse
Affiliation(s)
- Samira Ranjbar
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | | | | | | |
Collapse
|
66
|
Huang H, Vogel HJ. Structural basis for the activation of platelet integrin αIIbβ3 by calcium- and integrin-binding protein 1. J Am Chem Soc 2012; 134:3864-72. [PMID: 22283712 PMCID: PMC3290099 DOI: 10.1021/ja2111306] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Calcium and integrin binding protein 1 (CIB1) is a specific binding partner for the cytoplasmic domain of the αIIb subunit of the highly abundant platelet integrin αIIbβ3. This protein has been suggested to be involved in the regulation of the activation of αIIbβ3, a process leading to platelet aggregation and blood coagulation. In this work, the solution structure of the deuterated Ca(2+)-CIB1 protein complexed with an αIIb peptide was first determined through modern RDC-based NMR methods. Next, we generated a complex structure for CIB1 and the αIIb domain (Ca(2+)-CIB1/αIIb) using the program Haddock, which is based on experimental restraints obtained for the protein-peptide interface from cross-saturation NMR experiments. In this data-driven complex structure, the N-terminal α-helix of the cytoplasmic domain of αIIb is buried in the hydrophobic pocket of the C-lobe of Ca(2+)-CIB1. The C-terminal acidic tail of αIIb remains unstructured and likely interacts with several positively charged residues in the N-lobe of Ca(2+)-CIB1. A potential molecular mechanism for the CIB1-mediated activation of the platelet integrin could be proposed on the basis of the model structure of this protein complex. Another feature of this work is that, in the NMR cross-saturation experiments, we applied the selective radio frequency irradiation to the smaller binding partner (the αIIb peptide), and successfully detected the binding interface on the larger binding partner Ca(2+)-CIB1 through its selectively protonated methyl groups. This 'reverse' methodology has a broad potential to be employed to many other complexes where synthetic peptides and a suitably isotope-labeled medium- to large-sized protein are used to study protein-protein interactions.
Collapse
Affiliation(s)
- Hao Huang
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary (AB), Canada, T2N 1N4
| | | |
Collapse
|
67
|
Takeda M, Kainosho M. 1.12 Labeling Techniques. COMPREHENSIVE BIOPHYSICS 2012. [PMCID: PMC7151895 DOI: 10.1016/b978-0-12-374920-8.00116-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The current status of isotope-assisted multidimensional nuclear magnetic resonance (NMR) spectroscopy for protein structural studies is reviewed. After introducing various classic isotope labeling methods, some new emerging technologies, such as the stereo-array isotope labeling method, are described. The concomitant development of advanced stable isotope labeling strategies, NMR instrumentation, sophisticated NMR measurements, spectral analysis, and structural calculation algorithms is essential to overcome the current limitations restricting the use of protein NMR spectroscopy.
Collapse
|
68
|
Miyanoiri Y, Takeda M, Kainosho M. Stereo-Array Isotope Labeling Method for Studying Protein Structure and Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:83-93. [DOI: 10.1007/978-94-007-4954-2_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
69
|
Ward ME, Shi L, Lake E, Krishnamurthy S, Hutchins H, Brown LS, Ladizhansky V. Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin. J Am Chem Soc 2011; 133:17434-43. [PMID: 21919530 DOI: 10.1021/ja207137h] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We used high-resolution proton-detected multidimensional NMR to study the solvent-exposed parts of a seven-helical integral membrane proton pump, proteorhodopsin (PR). PR samples were prepared by growing the apoprotein on fully deuterated medium and reintroducing protons to solvent-accessible sites through exchange with protonated buffer. This preparation leads to NMR spectra with proton resolution down to ca. 0.2 ppm at fast spinning (28 kHz) in a protein back-exchanged at a level of 40%. Novel three-dimensional proton-detected chemical shift correlation spectroscopy allowed for the identification and resonance assignment of the solvent-exposed parts of the protein. Most of the observed residues are located at the membrane interface, but there are notable exceptions, particularly in helix G, where most of the residues are susceptible to H/D exchange. This helix contains Schiff base-forming Lys231, and many conserved polar residues in the extracellular half, such as Asn220, Tyr223, Asn224, Asp227, and Asn230. We proposed earlier that high mobility of the F-G loop may transiently expose a hydrophilic cavity in the extracellular half of the protein, similar to the one found in xanthorhodopsin. Solvent accessibility of helix G is in line with this hypothesis, implying that such a cavity may be a part of the proton-conducting pathway lined by this helix.
Collapse
Affiliation(s)
- Meaghan E Ward
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | | | | | | | | |
Collapse
|
70
|
Dutta K, Natarajan A, Nair PA, Shuman S, Ghose R. Sequence-specific 1H, 13C and 15N assignments of the phosphoesterase (PE) domain of Pseudomonas aeruginosa DNA ligase D (LigD). BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:151-155. [PMID: 21213076 PMCID: PMC4156853 DOI: 10.1007/s12104-010-9289-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 12/27/2010] [Indexed: 05/30/2023]
Abstract
DNA ligase D (LigD), consisting of polymerase, ligase and phosphoesterase domains, is the essential catalyst of the bacterial non-homologous end-joining pathway of DNA double-strand break repair. The phosphoesterase (PE) module performs manganese-dependent 3'-phosphomonoesterase and 3'-ribonucleoside resection reactions that heal broken ends in preparation for sealing. LigD PE exemplifies a structurally and mechanistically unique class of DNA end-processing enzymes. Here, we present the resonance assignments of the PE domain of Pseudomonas aeruginosa LigD comprising the N-terminal 177 residues.
Collapse
Affiliation(s)
- Kaushik Dutta
- The New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027
| | - Aswin Natarajan
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016
| | - Pravin A. Nair
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
| | - Ranajeet Ghose
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016
| |
Collapse
|
71
|
Piserchio A, Warthaka M, Devkota AK, Kaoud TS, Lee S, Abramczyk O, Ren P, Dalby KN, Ghose R. Solution NMR insights into docking interactions involving inactive ERK2. Biochemistry 2011; 50:3660-72. [PMID: 21449613 DOI: 10.1021/bi2000559] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The mitogen-activated protein (MAP) kinase ERK2 contains recruitment sites that engage canonical and noncanonical motifs found in a variety of upstream kinases, regulating phosphatases and downstream targets. Interactions involving two of these sites, the D-recruitment site (DRS) and the F-recruitment site (FRS), have been shown to play a key role in signal transduction by ERK/MAP kinases. The dynamic nature of these recruitment events makes NMR uniquely suited to provide significant insight into these interactions. While NMR studies of kinases in general have been greatly hindered by their large size and complex dynamic behavior leading to the suboptimal performance of standard methodologies, we have overcome these difficulties for inactive full-length ERK2 and obtained an acceptable level of backbone resonance assignments. This allowed a detailed investigation of the structural perturbations that accompany interactions involving both canonical and noncanonical recruitment events. No crystallographic information exists for the latter. We found that the chemical shift perturbations in inactive ERK2, indicative of structural changes in the presence of canonical and noncanonical motifs, are not restricted to the recruitment sites but also involve the linker that connects the N- and C-lobes and, in most cases, a gatekeeper residue that is thought to exert allosteric control over catalytic activity. We also found that, even though the canonical motifs interact with the DRS utilizing both charge-charge and hydrophobic interactions, the noncanonical interactions primarily involve the latter. These results demonstrate the feasibility of solution NMR techniques for a comprehensive analysis of docking interactions in a full-length ERK/MAP kinase.
Collapse
Affiliation(s)
- Andrea Piserchio
- Department of Chemistry, The City College of New York, New York, New York 10031, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
72
|
Reuther G, Harris R, Girvin M, Leyh TS. Backbone 1H, 13C, 15N NMR assignments of the unliganded and substrate ternary complex forms of mevalonate diphosphate decarboxylase from Streptococcus pneumoniae. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:11-14. [PMID: 20737255 PMCID: PMC3245623 DOI: 10.1007/s12104-010-9255-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
Mevalonate diphosphate decarboxylase (MDD) catalyzes the ATP-dependent decarboxylation of diphosphomevalonate (DPM) to produce isopentenyl diphosphate (IPP), the molecular "building block" for more than 25,000 distinct isoprenoids, including cholesterol, steroid hormones and terpenoids. Here, we present the first backbone assignment of Streptococcus pneumoniae MDD in the unliganded state and in a ternary complex with DPM and AMPPCP--a nucleotide analogue unable to transfer the γ-phosphoryl group. The secondary chemical shifts for the unliganded form are in good agreement with the crystal structure of Streptococcus pyogenes (~70% sequence identity). The addition of substrate and nucleotide to the enzyme results in chemical shift changes of cross peaks that correspond to residues in the binding pocket.
Collapse
Affiliation(s)
- Guido Reuther
- Department of Microbiology and Immunology, Albert-Einstein-College of Medicine of Yeshiva University, Bronx, NY 10461-1926, USA
| | | | | | | |
Collapse
|
73
|
De Biasio A, Sánchez R, Prieto J, Villate M, Campos-Olivas R, Blanco FJ. Reduced stability and increased dynamics in the human proliferating cell nuclear antigen (PCNA) relative to the yeast homolog. PLoS One 2011; 6:e16600. [PMID: 21364740 PMCID: PMC3041752 DOI: 10.1371/journal.pone.0016600] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 01/05/2011] [Indexed: 11/18/2022] Open
Abstract
Proliferating Cell Nuclear Antigen (PCNA) is an essential factor for DNA replication and repair. PCNA forms a toroidal, ring shaped structure of 90 kDa by the symmetric association of three identical monomers. The ring encircles the DNA and acts as a platform where polymerases and other proteins dock to carry out different DNA metabolic processes. The amino acid sequence of human PCNA is 35% identical to the yeast homolog, and the two proteins have the same 3D crystal structure. In this report, we give evidence that the budding yeast (sc) and human (h) PCNAs have highly similar structures in solution but differ substantially in their stability and dynamics. hPCNA is less resistant to chemical and thermal denaturation and displays lower cooperativity of unfolding as compared to scPCNA. Solvent exchange rates measurements show that the slowest exchanging backbone amides are at the β-sheet, in the structure core, and not at the helices, which line the central channel. However, all the backbone amides of hPCNA exchange fast, becoming undetectable within hours, while the signals from the core amides of scPCNA persist for longer times. The high dynamics of the α-helices, which face the DNA in the PCNA-loaded form, is likely to have functional implications for the sliding of the PCNA ring on the DNA since a large hole with a flexible wall facilitates the establishment of protein-DNA interactions that are transient and easily broken. The increased dynamics of hPCNA relative to scPCNA may allow it to acquire multiple induced conformations upon binding to its substrates enlarging its binding diversity.
Collapse
Affiliation(s)
| | | | - Jesús Prieto
- Structural and Computational Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | | | - Ramón Campos-Olivas
- Structural and Computational Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Francisco J. Blanco
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
74
|
Rao JN, Jao CC, Hegde BG, Langen R, Ulmer TS. A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins. J Am Chem Soc 2010; 132:8657-68. [PMID: 20524659 DOI: 10.1021/ja100646t] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially folded proteins, characterized as exhibiting secondary structure elements with loose or absent tertiary contacts, represent important intermediates in both physiological protein folding and pathological protein misfolding. To aid in the characterization of the structural state(s) of such proteins, a novel structure calculation scheme is presented that combines structural restraints derived from pulsed EPR and NMR spectroscopy. The methodology is established for the protein alpha-synuclein (alphaS), which exhibits characteristics of a partially folded protein when bound to a micelle of the detergent sodium lauroyl sarcosinate (SLAS). By combining 18 EPR-derived interelectron spin label distance distributions with NMR-based secondary structure definitions and bond vector restraints, interelectron distances were correlated and a set of theoretical ensemble basis populations was calculated. A minimal set of basis structures, representing the partially folded state of SLAS-bound alphaS, was subsequently derived by back-calculating correlated distance distributions. A surprising variety of well-defined protein-micelle interactions was thus revealed in which the micelle is engulfed by two differently arranged antiparallel alphaS helices. The methodology further provided the population ratios between dominant ensemble structural states, whereas limitation in obtainable structural resolution arose from spin label flexibility and residual uncertainties in secondary structure definitions. To advance the understanding of protein-micelle interactions, the present study concludes by showing that, in marked contrast to secondary structure stability, helix dynamics of SLAS-bound alphaS correlate with the degree of protein-induced departures from free micelle dimensions.
Collapse
Affiliation(s)
- Jampani Nageswara Rao
- Department of Biochemistry & Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, California 90033, USA
| | | | | | | | | |
Collapse
|
75
|
Poget SF, Harris R, Cahill SM, Girvin ME. 1H, 13C, 15N backbone NMR assignments of the Staphylococcus aureus small multidrug-resistance pump (Smr) in a functionally active conformation. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:139-42. [PMID: 20407887 PMCID: PMC2935522 DOI: 10.1007/s12104-010-9228-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 04/08/2010] [Indexed: 05/13/2023]
Abstract
The plasmid-encoded small multidrug resistance pump from S. aureus transports a variety of quaternary ammonium and other hydrophobic compounds, enhancing the bacterial host's resistance to common hospital disinfectants. The protein folds as a homo-dimer of four transmembrane helices each, and appears to be fully functional only in lipid bilayers. Here we report the backbone resonance assignments and implied secondary structure for (2)H(13)C(15)N Smr reconstituted into lipid bicelles. Significant changes were observed between the chemical shifts of the protein in lipid bicelles compared to those in detergent micelles.
Collapse
Affiliation(s)
- Sébastien F. Poget
- Chemistry Department, College of Staten Island, 2800 Victory Boulevard, Staten Island, NY 10314, USA
| | - Richard Harris
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Sean M. Cahill
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Mark E. Girvin
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| |
Collapse
|
76
|
Tang M, Comellas G, Mueller LJ, Rienstra CM. High resolution ¹³C-detected solid-state NMR spectroscopy of a deuterated protein. JOURNAL OF BIOMOLECULAR NMR 2010; 48:103-111. [PMID: 20803233 PMCID: PMC3044443 DOI: 10.1007/s10858-010-9442-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 07/30/2010] [Indexed: 05/27/2023]
Abstract
High resolution ¹³C-detected solid-state NMR spectra of the deuterated beta-1 immunoglobulin binding domain of the protein G (GB1) have been collected to show that all ¹⁵N, ¹³C', C¹³Cα and ¹³Cβ sites are resolved in C¹³C-¹³C and ¹⁵N-C¹³C spectra, with significant improvement in T(2) relaxation times and resolution at high magnetic field (750 MHz). The comparison of echo T(2) values between deuterated and protonated GB1 at various spinning rates and under different decoupling schemes indicates that ¹³Cα T(2)' times increase by almost a factor of two upon deuteration at all spinning rates and under moderate decoupling strength, and thus the deuteration enables application of scalar-based correlation experiments that are challenging from the standpoint of transverse relaxation, with moderate proton decoupling. Additionally, deuteration in large proteins is a useful strategy to selectively detect polar residues that are often important for protein function and protein-protein interactions.
Collapse
Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Leonard J. Mueller
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA. Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA. Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| |
Collapse
|
77
|
Butterwick JA, MacKinnon R. Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. J Mol Biol 2010; 403:591-606. [PMID: 20851706 DOI: 10.1016/j.jmb.2010.09.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 09/04/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
Voltage-sensor domains (VSDs) are specialized transmembrane segments that confer voltage sensitivity to many proteins such as ion channels and enzymes. The activities of these domains are highly dependent on both the chemical properties and the physical properties of the surrounding membrane environment. To learn about VSD-lipid interactions, we used nuclear magnetic resonance spectroscopy to determine the structure and phospholipid interface of the VSD from the voltage-dependent K(+) channel KvAP (prokaryotic Kv from Aeropyrum pernix). The solution structure of the KvAP VSD solubilized within phospholipid micelles is similar to a previously determined crystal structure solubilized by a nonionic detergent and complexed with an antibody fragment. The differences observed include a previously unidentified short amphipathic α-helix that precedes the first transmembrane helix and a subtle rigid-body repositioning of the S3-S4 voltage-sensor paddle. Using (15)N relaxation experiments, we show that much of the VSD, including the pronounced kink in S3 and the S3-S4 paddle, is relatively rigid on the picosecond-to-nanosecond timescale. In contrast, the kink in S3 is mobile on the microsecond-to-millisecond timescale and may act as a hinge in the movement of the paddle during channel gating. We characterized the VSD-phospholipid micelle interactions using nuclear Overhauser effect spectroscopy and showed that the micelle uniformly coats the KvAP VSD and approximates the chemical environment of a phospholipid bilayer. Using paramagnetically labeled phospholipids, we show that bilayer-forming lipids interact with the S3 and S4 helices more strongly than with S1 and S2.
Collapse
Affiliation(s)
- Joel A Butterwick
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
| | | |
Collapse
|
78
|
Huang C, Mohanty S. Challenging the limit: NMR assignment of a 31 kDa helical membrane protein. J Am Chem Soc 2010; 132:3662-3. [PMID: 20178386 PMCID: PMC2862971 DOI: 10.1021/ja100078z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural determination of membrane proteins by NMR spectroscopy remains a challenge, especially for helical membrane proteins. Here we report the NMR assignment and secondary structure of a 31 kDa helical membrane protein, the C-terminal domain of Stt3p. The C-terminal domain of Stt3p has been proposed to be the catalytic domain of yeast oligosaccharyl transferase (OT), a multisubunit membrane-associated enzyme complex catalyzing N-glycosylation, which is an essential and highly conserved protein modification. NMR assignment is the first critical step in the determination of the high-resolution solution structure and further structure-function studies.
Collapse
Affiliation(s)
- Chengdong Huang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Smita Mohanty
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| |
Collapse
|
79
|
Jacso T, Grote M, Daus ML, Schmieder P, Keller S, Schneider E, Reif B. Periplasmic loop P2 of the MalF subunit of the maltose ATP binding cassette transporter is sufficient to bind the maltose binding protein MalE. Biochemistry 2009; 48:2216-25. [PMID: 19159328 DOI: 10.1021/bi801376m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Escherichia coli maltose transporter belongs to the ATP binding cassette (ABC) transporter superfamily. Recently, the crystal structure of the full transporter MalFGK2 in complex with the maltose binding protein (MBP) was determined [Oldham, M. L., et al. (2007) Crystal structure of a catalytic intermediate of the maltose transporter. Nature 450, 515-522]. Using liquid-state NMR, we find that the periplasmic loop P2 of MalF (MalF-P2) folds independently in solution and adopts a well-defined tertiary structure which is similar to the one found in the crystal. MalF-P2 interacts with the maltose binding protein, independent of the transmembrane region of MalF and MalG with an affinity of 10-20 microM, in the presence and absence of substrate. Analysis of residual dipolar coupling (RDC) experiments shows that the conformation of the two individual domains of MalF-P2 is preserved in the absence of MalE and resembles the conformation in the X-ray structure. Upon titration of MalE to MalF-P2, the two domains of MalF-P2 change their relative orientation to accommodate the ligand. In particular, a conformational change of domain 2 of MalF-P2 is induced, which is distinct from the conformation found in the X-ray structure.
Collapse
Affiliation(s)
- Tomas Jacso
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
80
|
NMR reveals pathway for ferric mineral precursors to the central cavity of ferritin. Proc Natl Acad Sci U S A 2009; 107:545-50. [PMID: 20018746 DOI: 10.1073/pnas.0908082106] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ferritin is a multimeric nanocage protein that directs the reversible biomineralization of iron. At the catalytic ferroxidase site two iron(II) ions react with dioxygen to form diferric species. In order to study the pathway of iron(III) from the ferroxidase site to the central cavity a new NMR strategy was developed to manage the investigation of a system composed of 24 monomers of 20 kDa each. The strategy is based on (13)C-(13)C solution NOESY experiments combined with solid-state proton-driven (13)C-(13)C spin diffusion and 3D coherence transfer experiments. In this way, 75% of amino acids were recognized and 35% sequence-specific assigned. Paramagnetic broadening, induced by iron(III) species in solution (13)C-(13)C NOESY spectra, localized the iron within each subunit and traced the progression to the central cavity. Eight iron ions fill the 20-A-long iron channel from the ferrous/dioxygen oxidoreductase site to the exit into the cavity, inside the four-helix bundle of each subunit, contrasting with short paths in models. Magnetic susceptibility data support the formation of ferric multimers in the iron channels. Multiple iron channel exits are near enough to facilitate high concentration of iron that can mineralize in the ferritin cavity, illustrating advantages of the multisubunit cage structure.
Collapse
|
81
|
Mehrabi M, Ghobadi S, Khodarahmi R. Spectroscopic study on the interaction of celecoxib with human carbonic anhydrase II: Thermodynamic characterization of the binding process. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 97:161-8. [DOI: 10.1016/j.jphotobiol.2009.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 09/06/2009] [Accepted: 09/16/2009] [Indexed: 10/20/2022]
|
82
|
Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
| |
Collapse
|
83
|
Effect of pseudorepeat rearrangement on alpha-synuclein misfolding, vesicle binding, and micelle binding. J Mol Biol 2009; 390:516-29. [PMID: 19481090 DOI: 10.1016/j.jmb.2009.05.058] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/14/2009] [Accepted: 05/18/2009] [Indexed: 01/13/2023]
Abstract
The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructured conformations to structured conformations. Based on aS interactions with aggregation-inhibiting small molecules, an aS variant termed shuffled alpha-synuclein (SaS), wherein the first six pseudorepeats had been rearranged, was introduced. Here, the effects of this rearrangement on misfolding, vesicle binding, and micelle binding are examined in reference to aS and beta-synuclein to study the sequence characteristics underlying these processes. Fibrillization correlates with the distinct clustering of residues with high beta-sheet propensities, while vesicle affinities depend on the mode of pseudorepeat interchange and loss. In the presence of micelles, the pseudorepeat region of SaS adopts an essentially continuous helix, whereas aS and beta-synuclein encounter a distinct helix break, indicating that a more homogeneous distribution of surfactant affinities in SaS prevented the formation of an extensive helix break in the micelle-bound state. By demonstrating the importance of the distribution of beta-sheet propensities and by revealing inhomogeneous aS surfactant affinities, the present study provides novel insights into two central themes of synuclein biology.
Collapse
|
84
|
Keller N, Mares J, Zerbe O, Grütter MG. Structural and biochemical studies on procaspase-8: new insights on initiator caspase activation. Structure 2009; 17:438-48. [PMID: 19278658 DOI: 10.1016/j.str.2008.12.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 12/10/2008] [Accepted: 12/21/2008] [Indexed: 12/19/2022]
Abstract
Caspases are proteases with an active-site cysteine and aspartate specificity in their substrates. They are involved in apoptotic cell death and inflammation, and dysfunction of these enzymes is directly linked to a variety of diseases. Caspase-8 initiates an apoptotic pathway triggered by external stimuli. It was previously characterized in its active inhibitor bound state by crystallography. Here we present the solution structure of the monomeric unprocessed catalytic domain of the caspase-8 zymogen, procaspase-8, showing for the first time the position of the linker and flexibility of the active site forming loops. Biophysical studies of carefully designed mutants allowed disentangling dimerization and processing, and we could demonstrate lack of activity of monomeric uncleaved procaspase-8 and of a processed but dimerization-incompetent mutant. The data provide experimental support in so-far unprecedented detail, and reveal why caspase-8 (and most likely other initiator caspases) needs the dimerization platform during activation.
Collapse
Affiliation(s)
- Nadine Keller
- Institute of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | | | | | | |
Collapse
|
85
|
Sheppard D, Guo C, Tugarinov V. Methyl-detected 'out-and-back' NMR experiments for simultaneous assignments of Alabeta and Ilegamma2 methyl groups in large proteins. JOURNAL OF BIOMOLECULAR NMR 2009; 43:229-38. [PMID: 19274445 DOI: 10.1007/s10858-009-9305-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/09/2009] [Accepted: 02/18/2009] [Indexed: 05/23/2023]
Abstract
A set of sensitive methyl-detected 'out-and-back' NMR experiments for simultaneous assignments of Alabeta and Ilegamma2 methyl positions in large proteins is described. The developed methodology is applied to an 82-kDa enzyme Malate Synthase G. Complete alanine beta and isoleucine gamma2 1H-13C methyl chemical shift assignments could be obtained from the set of new methyl-detected 'out-and-back' 3D experiments. The described methodology for methyl assignments should be applicable to protein molecules within approximately 100-kDa molecular weight range irrespective of the labeling strategy chosen to produce selectively protonated Alabeta and Ilegamma2 13CH3 sites on a deuterated background.
Collapse
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | | | | |
Collapse
|
86
|
Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. JOURNAL OF BIOMOLECULAR NMR 2009; 43:63-78. [PMID: 19034676 PMCID: PMC2683404 DOI: 10.1007/s10858-008-9288-5] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 10/28/2008] [Indexed: 05/19/2023]
Abstract
NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.
Collapse
Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | | | | | | |
Collapse
|
87
|
Skinner AL, Laurence JS. High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands. J Pharm Sci 2009; 97:4670-95. [PMID: 18351634 DOI: 10.1002/jps.21378] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ability of a small molecule to bind and modify the activity of a protein target at a specific site greatly impacts the success of drugs in the pharmaceutical industry. One of the most important tools for evaluating these interactions has been high-field solution nuclear magnetic resonance (NMR) because of its unique ability to examine even weak protein-drug interactions at high resolution. NMR can be used to evaluate the structural, thermodynamic and kinetic aspects of a binding reaction. The basis of NMR screening experiments is that binding causes a perturbation in the physical properties of both molecules. Unique properties of small and macromolecules allow selective detection of either the protein target or ligand, even in a mixture of compounds. This review outlines current methodologies for assessing protein-ligand interactions from the perspectives of the protein target and ligand and delineates the fundamental principles for understanding NMR approaches in drug research. Advances in instrumentation, pulse sequences, isotopic labeling strategies, and the development of competition experiments support the study of higher molecular weight protein targets, facilitate higher-throughput and expand the range of binding affinities that can be evaluated, enhancing the utility of NMR for identifying and characterizing potential therapeutics to druggable protein targets.
Collapse
Affiliation(s)
- Andria L Skinner
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
| | | |
Collapse
|
88
|
Sheppard D, Guo C, Tugarinov V. 4D 1H−13C NMR Spectroscopy for Assignments of Alanine Methyls in Large and Complex Protein Structures. J Am Chem Soc 2009; 131:1364-5. [DOI: 10.1021/ja808202q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devon Sheppard
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Chenyun Guo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Vitali Tugarinov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| |
Collapse
|
89
|
Buchko GW, Sofia HJ. Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:25-28. [PMID: 19636916 DOI: 10.1007/s12104-007-9075-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 12/11/2007] [Indexed: 05/28/2023]
Abstract
Cyanothece 51142 contains a 78-residue protein, cce_0567, that falls into the DUF683 family of proteins associated with nitrogen fixation. Here we report the assignment of most of the main chain and 13C(beta) side chain resonances of the approximately 40 kDa homo-tetramer.
Collapse
Affiliation(s)
- Garry W Buchko
- Biological Sciences Division, Pacific Northwest National Laboratory, Mail-Stop K8-98, P.O. Box 999, Richland, WA 99352, USA.
| | | |
Collapse
|
90
|
Schwenk J, Zolles G, Kandias NG, Neubauer I, Kalbacher H, Covarrubias M, Fakler B, Bentrop D. NMR analysis of KChIP4a reveals structural basis for control of surface expression of Kv4 channel complexes. J Biol Chem 2008; 283:18937-46. [PMID: 18458082 DOI: 10.1074/jbc.m800976200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Potassium channel-interacting proteins (KChIPs) are EF-hand calcium-binding proteins of the recoverin/neuronal calcium sensor 1 family that co-assemble with the pore-forming Kv4 alpha-subunits and thus control surface trafficking of the voltage-gated potassium channels mediating the neuronal I(A) and cardiac I(to) currents. Different from the other KChIPs, KChIP4a largely reduces surface expression of the Kv4 channel complexes. Using solution NMR we show that the unique N terminus of KChIP4a forms a 6-turn alpha-helix that is connected to the highly conserved core of the KChIP protein via a solvent-exposed linker. As identified by chemical shift changes, N-terminal alpha-helix and core domain of KChIP4a interact with each other through the same hydrophobic surface pocket that is involved in intermolecular interaction between the N-terminal helix of Kv4alpha and KChIP in Kv4-KChIP complexes. Electrophysiological recordings and biochemical interaction assays of complexes formed by wild-type and mutant Kv4alpha and KChIP4a proteins suggest that competition of these two helical domains for the surface groove is responsible for the reduced trafficking of Kv4-KChIP4a complexes to the plasma membrane. Surface expression of Kv4 complexes may thus be controlled by an auto-inhibitory domain in the KChIP subunit.
Collapse
Affiliation(s)
- Jochen Schwenk
- Institute of Physiology II, University of Freiburg, D-79104 Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
91
|
Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 565] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| |
Collapse
|
92
|
Vlasie MD, Fernández-Busnadiego R, Prudêncio M, Ubbink M. Conformation of Pseudoazurin in the 152 kDa Electron Transfer Complex with Nitrite Reductase Determined by Paramagnetic NMR. J Mol Biol 2008; 375:1405-15. [DOI: 10.1016/j.jmb.2007.11.056] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 10/18/2007] [Accepted: 11/16/2007] [Indexed: 10/22/2022]
|
93
|
Burnley BT, Kalverda AP, Paisey SJ, Berry A, Homans SW. Hadamard NMR spectroscopy for relaxation measurements of large (>35 kDa) proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 39:239-45. [PMID: 17882509 DOI: 10.1007/s10858-007-9192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 08/31/2007] [Indexed: 05/17/2023]
Abstract
Here we present a suite of pulse sequences for the measurement of (15)N T(1), T(1rho) and NOE data that combine traditional TROSY-based pulse sequences with band-selective Hadamard frequency encoding. The additive nature of the Hadamard matrix produces much reduced resonance overlap without the need for an increase in the dimensionality of the experiment or a significant decrease in the signal to noise ratio. We validate the accuracy of these sequences in application to ubiquitin and demonstrate their utility for relaxation measurements in Escherichia coli Class II fructose 1,6-bisphosphate aldolase (FBP-aldolase), a 358 residue 78 kDa dimeric enzyme.
Collapse
Affiliation(s)
- B Tom Burnley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | | | | | | |
Collapse
|
94
|
Shen Y, Bax A. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. JOURNAL OF BIOMOLECULAR NMR 2007; 38:289-302. [PMID: 17610132 DOI: 10.1007/s10858-007-9166-6] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 05/16/2007] [Indexed: 05/05/2023]
Abstract
Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in phi/psi/chi(1 )torsion angles and sequence similarity to the query triplet of interest. The database contains (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C' chemical shifts for 200 proteins for which a high resolution X-ray (< or =2.4 A) structure is available. The relative importance of the weighting factors for the phi/psi/chi(1) angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C', respectively, including outliers.
Collapse
Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | | |
Collapse
|
95
|
Hu K, Vögeli B, Clore GM. Spin-state selective carbon-detected HNCO with TROSY optimization in all dimensions and double echo-antiecho sensitivity enhancement in both indirect dimensions. J Am Chem Soc 2007; 129:5484-91. [PMID: 17417840 DOI: 10.1021/ja067981l] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A carbon-detected TROSY-optimized experiment correlating 1HN, 15N, and 13C' resonances, referred to as c-TROSY-HNCO is presented, in which the 1HN and 15N TROSY effects are maintained in both indirect dimensions, while the directly detected 13C' is doubly TROSY-optimized with respect to 1HN and 15N. A new strategy for sensitivity enhancement, the so-called double echo-antiecho (dEA), is described and implemented in the c-TROSY-HNCO experiment. dEA offers sensitivity enhancement of square root of 2 in both indirect dimensions and is generally applicable to many multidimensional experiments. A carbon-detected HNCO experiment, c-HNCO, without TROSY optimization and sensitivity enhancement is also designed for comparison purposes. Relaxation simulations show that for a protein with a rotational correlation time of 10 ns or larger, the c-TROSY-HNCO experiment displays comparable or higher signal-to-noise (S/N) ratios than the c-HNCO experiment, although the former selects only 1/4 of the initial magnetization relative to the later. The high resolution afforded in the directly detected carbon dimension allows direct measurement of the doublet splitting to extract 1JCalphaC' scalar and 1DCalphaC' residual dipolar couplings. Simulations indicate that the c-TROSY-HNCO experiment offers higher precision (lower uncertainty) compared to the c-HNCO experiment for larger proteins. The experiments are applied to 15N/13C/2H/[Leu,Val]-methyl-protonated IIBMannose, a protein of molecular mass 18.6 kDa with a correlation time of approximately 10 ns at 30 degrees C. The experimental pairwise root-mean-square deviation for the measured 1JCalphaC' couplings obtained from duplicate experiments is 0.77 Hz. By directly measuring the doublet splitting, the experiments described here are expected to be much more tolerant to nonuniform values of 1JCalphaC' (or 1JCalphaC' + 1DCalphaC' for aligned samples) and pulse imperfections due to the smaller number of applied pulses in the "out-and-stay" coherence transfer in the c-HNCO-TROSY experiment relative to conventional 1H-detected "out-and-back" quantitative J correlation experiments. A carbon-detected TROSY-optimized experiment correlating 1HN, 15N, and 13C' resonances, referred to as c-TROSY-HNCO is presented, in which the 1HN and 15N TROSY effects are maintained in both indirect dimensions, while the directly detected 13C' is doubly TROSY-optimized with respect to 1HN and 15N. A new strategy for sensitivity enhancement, the so-called double echo-antiecho (dEA), is described and implemented in the c-TROSY-HNCO experiment. dEA offers sensitivity enhancement of in both indirect dimensions and is generally applicable to many multidimensional experiments.
Collapse
Affiliation(s)
- Kaifeng Hu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | | | | |
Collapse
|
96
|
Shimahara H, Yoshida T, Shibata Y, Shimizu M, Kyogoku Y, Sakiyama F, Nakazawa T, Tate SI, Ohki SY, Kato T, Moriyama H, Kishida KI, Tano Y, Ohkubo T, Kobayashi Y. Tautomerism of Histidine 64 Associated with Proton Transfer in Catalysis of Carbonic Anhydrase. J Biol Chem 2007; 282:9646-9656. [PMID: 17202139 DOI: 10.1074/jbc.m609679200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The imidazole (15)N signals of histidine 64 (His(64)), involved in the catalytic function of human carbonic anhydrase II (hCAII), were assigned unambiguously. This was accomplished by incorporating the labeled histidine as probes for solution NMR analysis, with (15)N at ring-N(delta1) and N(epsilon2), (13)Cat ring-Cepsilon1, (13)C and (15)N at all carbon and nitrogen, or (15)N at the amide nitrogen and the labeled glycine with (13)C at the carbonyl carbon. Using the pH dependence of ring-(15)N signals and a comparison between experimental and simulated curves, we determined that the tautomeric equilibrium constant (K(T)) of His(64) is 1.0, which differs from that of other histidine residues. This unique value characterizes the imidazole nitrogen atoms of His(64) as both a general acid (a) and base (b): its epsilon2-nitrogen as (a) releases one proton into the bulk, whereas its delta1-nitrogen as (b) extracts another proton from a water molecule within the water bridge coupling to the zinc-bound water inside the cave. This accelerates the generation of zinc-bound hydroxide to react with the carbon dioxide. Releasing the productive bicarbonate ion from the inside separates the water bridge pathway, in which the next water molecules move into beside zinc ion. A new water molecule is supplied from the bulk to near the delta1-nitrogen of His(64). These reconstitute the water bridge. Based on these features, we suggest here a catalytic mechanism for hCAII: the tautomerization of His(64) can mediate the transfers of both protons and water molecules at a neutral pH with high efficiency, requiring no time- or energy-consuming processes.
Collapse
Affiliation(s)
- Hideto Shimahara
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871; Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan
| | - Takuya Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Yasutaka Shibata
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Masato Shimizu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | - Yoshimasa Kyogoku
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | - Fumio Sakiyama
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | | | - Shin-Ichi Tate
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211
| | - Shin-Ya Ohki
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211
| | - Takeshi Kato
- Medical School Osaka University, Suita, Osaka 565-0871
| | | | | | - Yasuo Tano
- Medical School Osaka University, Suita, Osaka 565-0871
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Yuji Kobayashi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871; Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan.
| |
Collapse
|
97
|
Xu Y, Zheng Y, Fan JS, Yang D. A new strategy for structure determination of large proteins in solution without deuteration. Nat Methods 2007; 3:931-7. [PMID: 17060917 DOI: 10.1038/nmeth938] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 08/08/2006] [Indexed: 11/09/2022]
Abstract
So far high-resolution structure determination by nuclear magnetic resonance (NMR) spectroscopy has been limited to proteins <30 kDa, although global fold determination is possible for substantially larger proteins. Here we present a strategy for assigning backbone and side-chain resonances of large proteins without deuteration, with which one can obtain high-resolution structures from (1)H-(1)H distance restraints. The strategy uses information from through-bond correlation experiments to filter intraresidue and sequential correlations from through-space correlation experiments, and then matches the filtered correlations to obtain sequential assignment. We demonstrate this strategy on three proteins ranging from 24 to 65 kDa for resonance assignment and on maltose binding protein (42 kDa) and hemoglobin (65 kDa) for high-resolution structure determination. The strategy extends the size limit for structure determination by NMR spectroscopy to 42 kDa for monomeric proteins and to 65 kDa for differentially labeled multimeric proteins without the need for deuteration or selective labeling.
Collapse
Affiliation(s)
- Yingqi Xu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | | | | | | |
Collapse
|
98
|
Borbat PP, Freed JH. Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases. Methods Enzymol 2007; 423:52-116. [PMID: 17609127 DOI: 10.1016/s0076-6879(07)23003-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Applications of dipolar ESR spectroscopy to structural biology are rapidly expanding, and it has become a useful method that is aimed at resolving protein structure and functional mechanisms. The method of pulsed dipolar ESR spectroscopy (PDS) is outlined in the first half of the chapter, and it illustrates the simplicity and potential of this developing technology with applications to various biological systems. A more detailed description is presented of the implementation of PDS to reconstruct the ternary structure of a large dimeric protein complex from Thermotoga maritima, formed by the histidine kinase CheA and the coupling protein CheW. This protein complex is a building block of an extensive array composed of coupled supramolecular structures assembled from CheA/CheW proteins and transmembrane signaling chemoreceptors, which make up a sensor that is key to controlling the motility in bacterial chemotaxis. The reconstruction of the CheA/CheW complex has employed several techniques, including X-ray crystallography and pulsed ESR. Emphasis is on the role of PDS, which is part of a larger effort to reconstruct the entire signaling complex, including chemoreceptor, by means of PDS structural mapping. In order to precisely establish the mode of coupling of CheW to CheA and to globally map the complex, approximately 70 distances have already been determined and processed into molecular coordinates by readily available methods of distance geometry constraints.
Collapse
Affiliation(s)
- Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|
99
|
Quadt-Akabayov SR, Chill JH, Levy R, Kessler N, Anglister J. Determination of the human type I interferon receptor binding site on human interferon-alpha2 by cross saturation and an NMR-based model of the complex. Protein Sci 2006; 15:2656-68. [PMID: 17001036 PMCID: PMC2242419 DOI: 10.1110/ps.062283006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Type I interferons (IFNs) are a family of homologous helical cytokines that exhibit pleiotropic effects on a wide variety of cell types, including antiviral activity and antibacterial, antiprozoal, immunomodulatory, and cell growth regulatory functions. Consequently, IFNs are the human proteins most widely used in the treatment of several kinds of cancer, hepatitis C, and multiple sclerosis. All type I IFNs bind to a cell surface receptor consisting of two subunits, IFNAR1 and IFNAR2, associating upon binding of interferon. The structure of the extracellular domain of IFNAR2 (R2-EC) was solved recently. Here we study the complex and the binding interface of IFNalpha2 with R2-EC using multidimensional NMR techniques. NMR shows that IFNalpha2 does not undergo significant structural changes upon binding to its receptor, suggesting a lock-and-key mechanism for binding. Cross saturation experiments were used to determine the receptor binding site upon IFNalpha2. The NMR data and previously published mutagenesis data were used to derive a docking model of the complex with an RMSD of 1 Angstrom, and its well-defined orientation between IFNalpha2 and R2-EC and the structural quality greatly improve upon previously suggested models. The relative ligand-receptor orientation is believed to be important for interferon signaling and possibly one of the parameters that distinguish the different IFN I subtypes. This structural information provides important insight into interferon signaling processes and may allow improvement in the development of therapeutically used IFNs and IFN-like molecules.
Collapse
|
100
|
Zhang L, Yang D. SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins. Bioinformatics 2006; 22:2833-4. [PMID: 16966359 DOI: 10.1093/bioinformatics/btl477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED SCAssign (side-chain assignment) is a Sparky extension written in Python to assist the NMR resonance assignment of aliphatic side-chains of uniformly (13)C,(15)N-labeled large proteins. It is based on a general strategy recently developed in our laboratory that makes use of 4D (13)C,(15)N-edited NOESY, 3D MQ-(H)CC(m)H(m)-TOCSY, and prior backbone assignments. The program runs on all operating systems for which Sparky is available, and is easy to install, setup and use. Not only can it accelerate the assignment process, it also allows assignments of weak NOEs in 4D NOESY, which used to be very difficult with manual approach. AVAILABILITY The program, in the form of source code, is provided as free download at http://yangdw.science.nus.edu.sg/SCAssign. The website also contains installation guide, user manual and demonstrations recorded in Flash.
Collapse
Affiliation(s)
- Lei Zhang
- Graduate Program in Bioengineering, National University of Singapore 10 Medical Drive, 117597 Singapore
| | | |
Collapse
|