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McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. J Struct Biol X 2024; 10:100103. [PMID: 39035014 PMCID: PMC11255114 DOI: 10.1016/j.yjsbx.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric axially symmetric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring three-fold axial symmetry or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form binds and inhibits TRAP. We apply native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) to monitor the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we use solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP binding and inhibition.
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Affiliation(s)
- Craig A. McElroy
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elihu C. Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Melody L. Holmquist
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vibhuti Wadhwa
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- National Resource for Native MS-Guided Structural Biology, USA
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Mark P. Foster
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
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2
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McElroy C, Ihms E, Yadav DK, Holmquist M, Wadwha V, Wysocki V, Gollnick P, Foster M. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547145. [PMID: 37425951 PMCID: PMC10327191 DOI: 10.1101/2023.06.29.547145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring a three-helix bundle, or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form has been shown to bind and inhibit TRAP. We demonstrate the utility of native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) for monitoring the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we report the use of solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP inhibition.
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Affiliation(s)
- Craig McElroy
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Elihu Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Melody Holmquist
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vibhuti Wadwha
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- National Resource for Native MS-Guided Structural Biology
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo NY 14260
| | - Mark Foster
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
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3
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SAXS Reveals the Stabilization Effects of Modified Sugars on Model Proteins. Life (Basel) 2022; 12:life12010123. [PMID: 35054516 PMCID: PMC8778440 DOI: 10.3390/life12010123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/31/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Many proteins are usually not stable under different stresses, such as temperature and pH variations, mechanical stresses, high concentrations, and high saline contents, and their transport is always difficult, because they need to be maintained in a cold regime, which is costly and very challenging to achieve in remote areas of the world. For this reason, it is extremely important to find stabilizing agents that are able to preserve and protect proteins against denaturation. In the present work, we investigate, by extensively using synchrotron small-angle X-ray scattering experiments, the stabilization effect of five different sugar-derived compounds developed at ExtremoChem on two model proteins: myoglobin and insulin. The data analysis, based on a novel method that combines structural and thermodynamic features, has provided details about the physical-chemical processes that regulate the stability of these proteins in the presence of stabilizing compounds. The results clearly show that some modified sugars exert a greater stabilizing effect than others, being able to maintain the active forms of proteins at temperatures higher than those in which proteins, in the absence of stabilizers, reach denatured states.
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4
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Hydroxytyrosol Inhibits Protein Oligomerization and Amyloid Aggregation in Human Insulin. Int J Mol Sci 2020; 21:ijms21134636. [PMID: 32629793 PMCID: PMC7370040 DOI: 10.3390/ijms21134636] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 01/02/2023] Open
Abstract
Hydroxytyrosol (HT), one of the main phenolic components of olive oil, has attracted considerable interest for its biological properties, including a remarkable antioxidant and anti-inflammatory power and, recently, for its ability to interfere with the amyloid aggregation underlying several human diseases. We report here a broad biophysical approach and cell biology techniques that allowed us to characterize the molecular mechanisms by which HT affects insulin amyloid aggregation and the related cytotoxicity. Our data show that HT is able to fully inhibit insulin amyloid aggregation and this property seems to be ascribed to the stabilization of the insulin monomeric state. Moreover, HT completely reverses the toxic effect produced by amyloid insulin aggregates in neuroblastoma cell lines by fully inhibiting the production of toxic amyloid species. These findings suggest that the beneficial effects of olive oil polyphenols, including HT, may arise from multifunctional activities and suggest possible a application of this natural compound in the prevention or treatment of amyloid-associated diseases.
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Efimov SV, Zgadzay YO, Tarasova NB, Klochkov VV. Evidence of oligomerization of bovine insulin in solution given by NMR. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:881-889. [PMID: 29858914 DOI: 10.1007/s00249-018-1310-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/14/2018] [Accepted: 05/16/2018] [Indexed: 01/21/2023]
Abstract
The protein hormone insulin exists in several forms in nature, and a large number of modified sequences are used in pharmacy. They differ by physicochemical properties and efficiency of biological action. Pancreatic bovine insulin was studied in an acidic solution by nuclear magnetic resonance spectroscopy. [Formula: see text]H and [Formula: see text]C NMR signal assignment of backbone and side chains was made by analysis of a set of 2D spectra obtained on a sample with natural isotope abundance. The presence of certain secondary structure elements was revealed on a qualitative level based on nuclear Overhauser effect spectroscopy, which are similar to those observed in the crystal structure. The C-terminus of the B-chain possessed a remarkable flexibility. The molecule was shown to exist in exchange with oligomers based on its self-diffusion coefficient and correlation time measurements performed at different concentrations. Certain signals in the NOESY and HSQC spectra are consistent with the presence of minor conformers; this is an obstacle in simulating the molecular structure under the conditions used in the experiment.
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Affiliation(s)
- S V Efimov
- Laboratory of NMR spectroscopy, Institute of Physics, Kazan Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia.
| | - Yu O Zgadzay
- Laboratory of NMR spectroscopy, Institute of Physics, Kazan Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
| | - N B Tarasova
- Laboratory of Molecular Biology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2 Lobachevskiy St., Kazan, 420111, Russia
| | - V V Klochkov
- Laboratory of NMR spectroscopy, Institute of Physics, Kazan Federal University, 18 Kremlevskaya St., Kazan, 420008, Russia
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Mohanty J, Shinde MN, Barooah N, Bhasikuttan AC. Reversible Insulin Hexamer Assembly Promoted by Ethyl Violet: pH-Controlled Uptake and Release. J Phys Chem Lett 2016; 7:3978-3983. [PMID: 27661257 DOI: 10.1021/acs.jpclett.6b01745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Therapeutically improved long-acting insulin preparations require in-depth understanding of the hexamer assembly, structural selectivity, and its stability in solution. This Letter demonstrates, for the first time, an efficient method for the hexamerization of human insulin by a structure-specific triphenylmethane (TPM) dye, Ethyl Violet (EV), particularly, in the absence of Zn2+. Upon detailed spectroscopic evaluation and comparison with other TPM homologues, we establish that the diethylamino phenyl arms of EV are specific and effective in clipping the three dimer helices in a hexameric assembly. We establish that at physiological pH 7.4 and in the presence of the EV, insulin exists predominantly in its hexameric form, a condition appropriate for storage and preparation of long-acting insulin formulations. On the other hand, the disassembly of the hexamer into the monomeric form is accomplished at pH 5, highlighting its potential as a delivery vehicle for such custom-modified dyes/drugs.
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Affiliation(s)
- Jyotirmayee Mohanty
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
- Homi Bhabha National Institute , Training School Complex, Anushaktinagar, Mumbai 400 094, India
| | - Meenakshi N Shinde
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
- Student, BARC-SPPU PhD Program, Department of Chemistry, Savitribai Phule Pune University , Pune 411 007, India
| | - Nilotpal Barooah
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
| | - Achikanath C Bhasikuttan
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
- Homi Bhabha National Institute , Training School Complex, Anushaktinagar, Mumbai 400 094, India
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Vashisth H. Theoretical and computational studies of peptides and receptors of the insulin family. MEMBRANES 2015; 5:48-83. [PMID: 25680077 PMCID: PMC4384091 DOI: 10.3390/membranes5010048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Synergistic interactions among peptides and receptors of the insulin family are required for glucose homeostasis, normal cellular growth and development, proliferation, differentiation and other metabolic processes. The peptides of the insulin family are disulfide-linked single or dual-chain proteins, while receptors are ligand-activated transmembrane glycoproteins of the receptor tyrosine kinase (RTK) superfamily. Binding of ligands to the extracellular domains of receptors is known to initiate signaling via activation of intracellular kinase domains. While the structure of insulin has been known since 1969, recent decades have seen remarkable progress on the structural biology of apo and liganded receptor fragments. Here, we review how this useful structural information (on ligands and receptors) has enabled large-scale atomically-resolved simulations to elucidate the conformational dynamics of these biomolecules. Particularly, applications of molecular dynamics (MD) and Monte Carlo (MC) simulation methods are discussed in various contexts, including studies of isolated ligands, apo-receptors, ligand/receptor complexes and intracellular kinase domains. The review concludes with a brief overview and future outlook for modeling and computational studies in this family of proteins.
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Affiliation(s)
- Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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Heldin E, Grönlund S, Shanagar J, Hallgren E, Eriksson K, Xavier M, Tunes H, Vilela L. Development of an intermediate chromatography step in an insulin purification process. The use of a High Throughput Process Development approach based on selectivity parameters. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 973C:126-132. [PMID: 25464105 DOI: 10.1016/j.jchromb.2014.09.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 11/15/2022]
Abstract
Recent innovations in designing purification processes for biopharmaceutical production have enabled initial screening (optimization) of chromatographic conditions for binding to be performed in miniaturized batch format. The present report demonstrates the possibility of using this format to screen for selectivity and illustrates the need for careful adjustment of protocols when highly abundant, tightly-binding impurities are present in the sample. This batch format approach was used to choose a chromatography medium (resin) from a selection of available resins for the purification of recombinant insulin expressed in E. coli and to screen binding and elution conditions. Subsequent optimization was performed in small packed columns using a Design of Experiments (DoE) approach with statistical modeling before scaling up to a small pilot scale experiment. In this study insulin was effectively purified from the more tightly-binding C-peptide, and a reduction in insulin variants was also noted using the optimized conditions.
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Affiliation(s)
- Eva Heldin
- GE Healthcare, Björkgatan 30, 751 84 Uppsala, Sweden.
| | - Sara Grönlund
- GE Healthcare, Björkgatan 30, 751 84 Uppsala, Sweden
| | | | | | | | - Mariza Xavier
- BIOMM S.A. Praça Carlos Chagas, 49-8th Floor, Belo Horizonte, MG CEP 30170-020, Brazil
| | - Heloisa Tunes
- BIOMM S.A. Praça Carlos Chagas, 49-8th Floor, Belo Horizonte, MG CEP 30170-020, Brazil
| | - Luciano Vilela
- BIOMM S.A. Praça Carlos Chagas, 49-8th Floor, Belo Horizonte, MG CEP 30170-020, Brazil
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9
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Salbo R, Bush MF, Naver H, Campuzano I, Robinson CV, Pettersson I, Jørgensen TJD, Haselmann KF. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1181-1193. [PMID: 22499193 DOI: 10.1002/rcm.6211] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE The collision cross-section (Ω) of a protein or protein complex ion can be measured using traveling-wave (T-wave) ion mobility (IM) mass spectrometry (MS) via calibration with compounds of known Ω. The T-wave Ω-values depend strongly on instrument parameters and calibrant selection. Optimization of instrument parameters and calibration standards are crucial for obtaining accurate T-wave Ω-values. METHODS Human insulin and the fast-acting insulin aspart under native-like conditions (ammonium acetate, physiological pH) were analyzed on Waters SYNAPT G1 and G2 HDMS instruments. The calibrated T-wave Ω-values of insulin monomer, dimer, and hexamer ions were measured using many different combinations of denatured and native-like calibrants (masses between 2.85 and 256 kDa) and T-wave conditions. Drift-tube Ω-values were obtained on a modified SYNAPT G1. RESULTS Insulin T-wave Ω-values were measured at 26 combinations of T-wave velocity and amplitude. Optimal sets of calibrants were identified that yield Ω-values with minimal dependence on T-wave conditions and calibration plots with high R(2)-values. The T-wave Ω-values determined under conditions satisfying these criteria had absolute errors <2%. Structural differences between human insulin and fast-acting insulin aspart were probed with IM-MS. Insulin aspart monomers have increased flexibility, while hexamers are more compact than human insulin. CONCLUSIONS Accurate T-wave Ω-values that are indistinguishable from drift-tube values are obtained when using (1) native-like calibrants with masses that closely bracket that of the analyte, (2) T-wave velocities that maximize the R(2) of the calibration plot for those calibrants, and (3) at least three replicates at T-wave velocities that yield calibration plots with high R(2).
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Affiliation(s)
- Rune Salbo
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
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10
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The detection and quantitation of protein oligomerization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:19-41. [PMID: 22949109 DOI: 10.1007/978-1-4614-3229-6_2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There are many different techniques available to biologists and biochemists that can be used to detect and characterize the self-association of proteins. Each technique has strengths and weaknesses and it is often useful to combine several approaches to maximize the former and minimize the latter. Here we review a range of methodologies that identify protein self-association and/or allow the stoichiometry and affinity of the interaction to be determined, placing an emphasis on what type of information can be obtained and outlining the advantages and disadvantages involved. In general, in vitro biophysical techniques, such as size exclusion chromatography, analytical ultracentrifugation, scattering techniques, NMR spectroscopy, isothermal titration calorimetry, fluorescence anisotropy and mass spectrometry, provide information on stoichiometry and/or binding affinities. Other approaches such as cross-linking, fluorescence methods (e.g., fluorescence correlation spectroscopy, FCS; Förster resonance energy transfer, FRET; fluorescence recovery after photobleaching, FRAP; and proximity imaging, PRIM) and complementation approaches (e.g., yeast two hybrid assays and bimolecular fluorescence complementation, BiFC) can be used to detect protein self-association in a cellular context.
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11
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Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR. A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. J Comput Biol 2011; 18:1507-23. [PMID: 22035328 DOI: 10.1089/cmb.2011.0173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a primary tool to perform structural studies of proteins in physiologically-relevant solution conditions. Restraints on distances between pairs of nuclei in the protein, derived from the nuclear Overhauser effect (NOE), provide information about the structure of the protein in its folded state. NMR studies of symmetric protein homo-oligomers present a unique challenge. Using X-filtered NOESY experiments, it is possible to determine whether an NOE restrains a pair of protons across different subunits or within a single subunit, but current experimental techniques are unable to determine in which subunits the restrained protons lie. Consequently, it is difficult to assign NOEs to particular pairs of subunits with certainty, thus hindering the structural analysis of the oligomeric state. Computational approaches are needed to address this subunit ambiguity, but traditional solutions often rely on stochastic search coupled with simulated annealing and simulations of simplified molecular dynamics, which have many tunable parameters that must be chosen carefully and can also fail to report structures consistent with the experimental restraints. In addition, these traditional approaches rarely provide guarantees on running time or solution quality. We reduce the structure determination of homo-oligomers with cyclic symmetry to computing geometric arrangements of unions of annuli in a plane. Our algorithm, disco, runs in expected O(n²) time, where n is the number of distance restraints, potentially assigned ambiguously. disco is guaranteed to report the exact set of oligomer structures consistent with the distance restraints and also with orientational restraints from residual dipolar couplings (RDCs). We demonstrate our method using two symmetric protein complexes: the trimeric E. coli diacylglycerol kinase (DAGK) and a dimeric mutant of the immunoglobulin-binding domain B1 of streptococcal protein G (GB1). In both cases, disco computes oligomer structures with high precision and also finds distance restraints that are either mutually inconsistent or inconsistent with the RDCs. The entire protocol DISCO has been completely automated in a software package that is freely available and open-source at www.cs.duke.edu/donaldlab/software.php.
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Affiliation(s)
- Jeffrey W Martin
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
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12
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Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR. A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. Protein Sci 2011; 20:970-85. [PMID: 21413097 DOI: 10.1002/pro.620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 02/22/2011] [Accepted: 02/23/2011] [Indexed: 11/09/2022]
Abstract
High-resolution structure determination of homo-oligomeric protein complexes remains a daunting task for NMR spectroscopists. Although isotope-filtered experiments allow separation of intermolecular NOEs from intramolecular NOEs and determination of the structure of each subunit within the oligomeric state, degenerate chemical shifts of equivalent nuclei from different subunits make it difficult to assign intermolecular NOEs to nuclei from specific pairs of subunits with certainty, hindering structural analysis of the oligomeric state. Here, we introduce a graphical method, DISCO, for the analysis of intermolecular distance restraints and structure determination of symmetric homo-oligomers using residual dipolar couplings. Based on knowledge that the symmetry axis of an oligomeric complex must be parallel to an eigenvector of the alignment tensor of residual dipolar couplings, we can represent distance restraints as annuli in a plane encoding the parameters of the symmetry axis. Oligomeric protein structures with the best restraint satisfaction correspond to regions of this plane with the greatest number of overlapping annuli. This graphical analysis yields a technique to characterize the complete set of oligomeric structures satisfying the distance restraints and to quantitatively evaluate the contribution of each distance restraint. We demonstrate our method for the trimeric E. coli diacylglycerol kinase, addressing the challenges in obtaining subunit assignments for distance restraints. We also demonstrate our method on a dimeric mutant of the immunoglobulin-binding domain B1 of streptococcal protein G to show the resilience of our method to ambiguous atom assignments. In both studies, DISCO computed oligomer structures with high accuracy despite using ambiguously assigned distance restraints.
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Affiliation(s)
- Jeffrey W Martin
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
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13
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Pillon NJ, Vella RE, Soulère L, Becchi M, Lagarde M, Soulage CO. Structural and Functional Changes in Human Insulin Induced by the Lipid Peroxidation Byproducts 4-Hydroxy-2-nonenal and 4-Hydroxy-2-hexenal. Chem Res Toxicol 2011; 24:752-62. [DOI: 10.1021/tx200084d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicolas J. Pillon
- Université de Lyon, F-69600, Oullins, France
- INSERM UMR 1060, CarMeN, F-69621, Villeurbanne, France
- INSA-Lyon, IMBL, F-69621, Villeurbanne, France
- INRA U1235, F-69600, Oullins, France
| | - Roxane E. Vella
- Université de Lyon, F-69600, Oullins, France
- INSERM UMR 1060, CarMeN, F-69621, Villeurbanne, France
- INSA-Lyon, IMBL, F-69621, Villeurbanne, France
- INRA U1235, F-69600, Oullins, France
| | - Laurent Soulère
- Université de Lyon, F-69600, Oullins, France
- Laboratoire de Chimie Organique et Bioorganique, INSA-LYON, CNRS UMR 5246, ICBMS, F-69622, Villeurbanne, France
| | - Michel Becchi
- Université de Lyon, F-69600, Oullins, France
- CNRS UMS 3444, CCMP, F-69367 Lyon, France
| | - Michel Lagarde
- Université de Lyon, F-69600, Oullins, France
- INSERM UMR 1060, CarMeN, F-69621, Villeurbanne, France
- INSA-Lyon, IMBL, F-69621, Villeurbanne, France
- INRA U1235, F-69600, Oullins, France
| | - Christophe O. Soulage
- Université de Lyon, F-69600, Oullins, France
- INSERM UMR 1060, CarMeN, F-69621, Villeurbanne, France
- INSA-Lyon, IMBL, F-69621, Villeurbanne, France
- INRA U1235, F-69600, Oullins, France
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14
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Fernandez-Lima FA, Blase RC, Russell DH. A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2010; 298:111-118. [PMID: 21503273 PMCID: PMC3077763 DOI: 10.1016/j.ijms.2009.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we report ion-helium collision cross sections (CCS) for a number of peptide, small protein, and peptide/protein ionic complexes. The CCS values reported here are compared to previously reported results.[1, 2] We also compare values for low charge state species, i.e., [M + H](+) and [M + 2H](2+), formed by MALDI with values for high charge state species formed by ESI, and the measured CCSs are compared with predicted CCS for solid-state and solution phase structures and calculated structures obtained by using a protein-protein structure algorithm generator, based on a combined Biomolecular complex Generation with Global Evaluation and Ranking[3] and Multi Dimensional Scaling[4].
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15
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Yang Y, Petkova A, Huang K, Xu B, Hua QX, Ye IJ, Chu YC, Hu SQ, Phillips NB, Whittaker J, Ismail-Beigi F, Mackin RB, Katsoyannis PG, Tycko R, Weiss MA. An Achilles' heel in an amyloidogenic protein and its repair: insulin fibrillation and therapeutic design. J Biol Chem 2010; 285:10806-21. [PMID: 20106984 PMCID: PMC2856287 DOI: 10.1074/jbc.m109.067850] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 01/19/2010] [Indexed: 11/06/2022] Open
Abstract
Insulin fibrillation provides a model for a broad class of amyloidogenic diseases. Conformational distortion of the native monomer leads to aggregation-coupled misfolding. Whereas beta-cells are protected from proteotoxicity by hexamer assembly, fibrillation limits the storage and use of insulin at elevated temperatures. Here, we have investigated conformational distortions of an engineered insulin monomer in relation to the structure of an insulin fibril. Anomalous (13)C NMR chemical shifts and rapid (15)N-detected (1)H-(2)H amide-proton exchange were observed in one of the three classical alpha-helices (residues A1-A8) of the hormone, suggesting a conformational equilibrium between locally folded and unfolded A-chain segments. Whereas hexamer assembly resolves these anomalies in accordance with its protective role, solid-state (13)C NMR studies suggest that the A-chain segment participates in a fibril-specific beta-sheet. Accordingly, we investigated whether helicogenic substitutions in the A1-A8 segment might delay fibrillation. Simultaneous substitution of three beta-branched residues (Ile(A2) --> Leu, Val(A3) --> Leu, and Thr(A8) --> His) yielded an analog with reduced thermodynamic stability but marked resistance to fibrillation. Whereas amide-proton exchange in the A1-A8 segment remained rapid, (13)Calpha chemical shifts exhibited a more helical pattern. This analog is essentially without activity, however, as Ile(A2) and Val(A3) define conserved receptor contacts. To obtain active analogs, substitutions were restricted to A8. These analogs exhibit high receptor-binding affinity; representative potency in a rodent model of diabetes mellitus was similar to wild-type insulin. Although (13)Calpha chemical shifts remain anomalous, significant protection from fibrillation is retained. Together, our studies define an "Achilles' heel" in a globular protein whose repair may enhance the stability of pharmaceutical formulations and broaden their therapeutic deployment in the developing world.
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Affiliation(s)
- Yanwu Yang
- From the Departments of Biochemistry and
| | - Aneta Petkova
- the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Kun Huang
- From the Departments of Biochemistry and
| | - Bin Xu
- From the Departments of Biochemistry and
| | | | - I-Ju Ye
- From the Departments of Biochemistry and
| | - Ying-Chi Chu
- the Department of Pharmacology and Biological Chemistry, Mt. Sinai School of Medicine, New York University, New York, New York 10029, and
| | | | | | | | | | - Robert B. Mackin
- the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Panayotis G. Katsoyannis
- the Department of Pharmacology and Biological Chemistry, Mt. Sinai School of Medicine, New York University, New York, New York 10029, and
| | - Robert Tycko
- the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Michael A. Weiss
- From the Departments of Biochemistry and
- Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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16
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Bardiaux B, Bernard A, Rieping W, Habeck M, Malliavin TE, Nilges M. Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA. Proteins 2009; 75:569-85. [DOI: 10.1002/prot.22268] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Laughton CA, Orozco M, Vranken W. COCO: A simple tool to enrich the representation of conformational variability in NMR structures. Proteins 2008; 75:206-16. [DOI: 10.1002/prot.22235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex. Biophys J 2008; 95:4193-204. [PMID: 18676643 DOI: 10.1529/biophysj.108.139675] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cooperative binding of phenolic species to insulin hexamers is known to stabilize pharmaceutical preparations of the hormone. Phenol dissociation is rapid on hexamer dissolution timescales, and phenol unbinding upon dilution is likely the first step in the conversion of (pharmaceutical) hexameric insulin to the active monomeric form upon injection. However, a clear understanding of the determinants of the rates of phenol unbinding remains obscure, chiefly because residues implicated in phenol exchange as determined by NMR are not all associated with likely unbinding routes suggested by the best-resolved hexamer structures. We apply random acceleration molecular dynamics simulation to identify potential escape routes of phenol from hydrophobic cavities in the hexameric insulin-phenol complex. We find three major pathways, which provide new insights into (un)binding mechanisms for phenol. We identify several residues directly participating in escape events that serve to resolve ambiguities from recent NMR experiments. Reaction coordinates for dissociation of phenol are developed based on these exit pathways. Potentials of mean force along the reaction coordinate for each pathway are resolved using multiple independent steered molecular dynamics simulations with second-order cumulant expansion of Jarzynski's equality. Our results for DeltaF agree reasonably well within the range of known experimental and previous simulation magnitudes of this quantity. Based on structural analysis and energetic barriers for each pathway, we suggest a plausible preferred mechanism of phenolic exchange that differs from previous mechanisms. Several weakly-bound metastable states are also observed for the first time in the phenol dissociation reaction.
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19
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Potluri S, Yan AK, Donald BR, Bailey-Kellogg C. A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Protein Sci 2007; 16:69-81. [PMID: 17192589 PMCID: PMC2222843 DOI: 10.1110/ps.062427307] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Assignment of nuclear Overhauser effect (NOE) data is a key bottleneck in structure determination by NMR. NOE assignment resolves the ambiguity as to which pair of protons generated the observed NOE peaks, and thus should be restrained in structure determination. In the case of intersubunit NOEs in symmetric homo-oligomers, the ambiguity includes both the identities of the protons within a subunit, and the identities of the subunits to which they belong. This paper develops an algorithm for simultaneous intersubunit NOE assignment and C(n) symmetric homo-oligomeric structure determinations, given the subunit structure. By using a configuration space framework, our algorithm guarantees completeness, in that it identifies structures representing, to within a user-defined similarity level, every structure consistent with the available data (ambiguous or not). However, while our approach is complete in considering all conformations and assignments, it avoids explicit enumeration of the exponential number of combinations of possible assignments. Our algorithm can draw two types of conclusions not possible under previous methods: (1) that different assignments for an NOE would lead to different structural classes, or (2) that it is not necessary to uniquely assign an NOE, since it would have little impact on structural precision. We demonstrate on two test proteins that our method reduces the average number of possible assignments per NOE by a factor of 2.6 for MinE and 4.2 for CCMP. It results in high structural precision, reducing the average variance in atomic positions by factors of 1.5 and 3.6, respectively.
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Affiliation(s)
- Shobha Potluri
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
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20
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Inaba T, Tsunekawa N, Hirano T, Yoshihiro T, Kashiwagi H, Sato F. Density functional calculation of the electronic structure on insulin hexamer. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Inaba T, Sato F. Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules. J Comput Chem 2007; 28:984-95. [PMID: 17269119 DOI: 10.1002/jcc.20549] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We developed a new parallel density-functional canonical molecular-orbital program for large molecules based on the resolution of the identity method. In this study, all huge matrices were decomposed and saved to the distributed local memory. The routines of the analytical molecular integrals and numerical integrals of the exchange-correlation terms were parallelized using the single program multiple data method. A conventional linear algebra matrix library, ScaLAPACK, was used for matrix operations, such as diagonalization, multiplication, and inversion. Anderson's mixing method was adopted to accelerate the self-consistent field (SCF) convergence. Using this program, we calculated the canonical wavefunctions of a 306-residue protein, insulin hexamer (26,790 orbitals), and a 133-residue protein, interleukin (11,909 orbitals) by the direct-SCF method. In regard to insulin hexamer, the total parallelization efficiency of the first SCF iteration was estimated to be 82% using 64 Itanium 2 processors connected at 3.2 GB/s (SGI Altix3700), and the calculation successfully converged at the 17-th SCF iteration. By adopting the update method, the computational time of the first and the final SCF loops was 229 min and 156 min, respectively. The whole computational time including the calculation before the SCF loop was 2 days and 17 h. This study put the calculations of the canonical wavefunction of 30,000 orbitals to practical use.
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Affiliation(s)
- Toru Inaba
- Mechanical Engineering Research Laboratory, Hitachi Ltd., Japan
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22
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Potluri S, Yan AK, Chou JJ, Donald BR, Bailey-Kellogg C. Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins 2006; 65:203-19. [PMID: 16897780 DOI: 10.1002/prot.21091] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data-driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C(n) homo-oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level. For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 A, and variance in backbone atomic coordinates is an average of 12.32 A(2). Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 A and an average backbone variance of 6.80 A(2). By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo-oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo-oligomeric complex structures.
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Affiliation(s)
- Shobha Potluri
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA
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23
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Shafqat J, Melles E, Sigmundsson K, Johansson BL, Ekberg K, Alvelius G, Henriksson M, Johansson J, Wahren J, Jörnvall H. Proinsulin C-peptide elicits disaggregation of insulin resulting in enhanced physiological insulin effects. Cell Mol Life Sci 2006; 63:1805-11. [PMID: 16845606 PMCID: PMC2773842 DOI: 10.1007/s00018-006-6204-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using surface plasmon resonance (SPR) and electrospray mass spectrometry (ESI-MS), proinsulin C-peptide was found to influence insulin-insulin interactions. In SPR with chip-bound insulin, C-peptide mixed with analyte insulin increased the binding, while alone C-peptide did not. A control peptide with the same residues in random sequence had little effect. In ESI-MS, C-peptide lowered the presence of insulin hexamer. The data suggest that C-peptide promotes insulin disaggregation. Insulin/insulin oligomer muM dissociation constants were determined. Compatible with these findings, type 1 diabetic patients receiving insulin and C-peptide developed 66% more stimulation of glucose metabolism than when given insulin alone. A role of C-peptide in promoting insulin disaggregation may be important physiologically during exocytosis of pancreatic beta-cell secretory granulae and pharmacologically at insulin injection sites. It is compatible with the normal co-release of C-peptide and insulin and may contribute to the beneficial effect of C-peptide and insulin replacement in type 1 diabetics.
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Affiliation(s)
- J. Shafqat
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - E. Melles
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - K. Sigmundsson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Present Address: Departments of Cancer & ImmunoBiology, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - B. -L. Johansson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - K. Ekberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - G. Alvelius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - M. Henriksson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - J. Johansson
- Department of Molecular Biosciences, Swedish University of Agricultural Sciences, The Biomedical Centre, 751 23 Uppsala, Sweden
| | - J. Wahren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - H. Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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24
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Metz B, Kersten GFA, Baart GJE, de Jong A, Meiring H, ten Hove J, van Steenbergen MJ, Hennink WE, Crommelin DJA, Jiskoot W. Identification of Formaldehyde-Induced Modifications in Proteins: Reactions with Insulin. Bioconjug Chem 2006; 17:815-22. [PMID: 16704222 DOI: 10.1021/bc050340f] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formaldehyde is frequently used to inactivate, stabilize, or immobilize proteins. The treatment results in a large variety of chemical modifications in proteins, such as the formation of methylol groups, Schiff bases, and methylene bridges. The purpose of the present study was to identify the stable formaldehyde-induced modifications in a small protein. Therefore, insulin was treated with excess formaldehyde (CH2O) or deuterated formaldehyde (CD2O). In a separate experiment, insulin was modified by formaldehyde (CH2O vs CD2O) and glycine. The mixture of CH2O-treated and CD2O-treated insulin was digested by the proteinase Glu-C. The peptide fragments obtained were analyzed by liquid chromatography-mass spectrometry (LC-MS). Seven intramolecular cross-links were identified in formaldehyde-treated insulin. Furthermore, eight out of the sixteen potentially reactive sites of the insulin molecule were modified by incubation with formaldehyde and glycine. Both the location and the chemical nature of the modifications could be assigned based on the mass increase of potential adducts as elucidated in our previous study (B. Metz et al. (2004) J. Biol. Chem. 279, 6235-6243). To confirm the assigned structures, LC-MS measurements with collision-induced dissociation (LC-MS/MS) were performed on insulin fragments. The results of the LC-MS/MS analyses agreed excellently with the assignments. The study showed that arginine, tyrosine, and lysine residues were very reactive. However, eight theoretically reactive residues did not show detectable modifications, probably because of their low intrinsic reactivity, inaccessibility, or both. The asparagine, glutamine, and histidine residues were not converted in insulin. The N-termini of insulin were partly converted to the expected imidazolidinone adducts, indicating that the protein conformation affects the accessibility and reactivity of these residues. In conclusion, this study shows that, based on our current insights in the chemistry of the reactions between proteins and formaldehyde, we are able to elucidate the location and nature of formaldehyde-induced modifications in a small protein. The approach followed in this study may be generally applicable to larger formaldehyde-treated proteins, such as toxoids used in vaccines.
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Affiliation(s)
- Bernard Metz
- Unit Research and Development, The Netherlands Vaccine Institute (NVI), Bilthoven, The Netherlands.
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25
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Wan ZL, Huang K, Xu B, Hu SQ, Wang S, Chu YC, Katsoyannis PG, Weiss MA. Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant InsulinWakayama†,‡. Biochemistry 2005; 44:5000-16. [PMID: 15794638 DOI: 10.1021/bi047585k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Naturally occurring mutations in insulin associated with diabetes mellitus identify critical determinants of its biological activity. Here, we describe the crystal structure of insulin Wakayama, a clinical variant in which a conserved valine in the A chain (residue A3) is substituted by leucine. The substitution occurs within a crevice adjoining the classical receptor-binding surface and impairs receptor binding by 500-fold, an unusually severe decrement among mutant insulins. To resolve whether such decreased activity is directly or indirectly mediated by the variant side chain, we have determined the crystal structure of Leu(A3)-insulin and investigated the photo-cross-linking properties of an A3 analogue containing p-azidophenylalanine. The structure, characterized in a novel crystal form as an R(6) zinc hexamer at 2.3 A resolution, is essentially identical to that of the wild-type R(6) hexamer. The variant side chain remains buried in a nativelike crevice with small adjustments in surrounding side chains. The corresponding photoactivatable analogue, although of low affinity, exhibits efficient cross-linking to the insulin receptor. The site of photo-cross-linking lies within a 14 kDa C-terminal domain of the alpha-subunit. This domain, unrelated in sequence to the major insulin-binding region in the N-terminal L1 beta-helix, is also contacted by photoactivatable probes at positions A8 and B25. Packing of Val(A3) at this interface may require a conformational change in the B chain to expose the A3-related crevice. The structure of insulin Wakayama thus evokes the reasoning of Sherlock Holmes in "the curious incident of the dog in the night": the apparent absence of structural perturbations (like the dog that did not bark) provides a critical clue to the function of a hidden receptor-binding surface.
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Affiliation(s)
- Zhu-li Wan
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4935, USA
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26
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Roy SS, Mukherjee M, Bhattacharya S, Mandal CN, Kumar LR, Dasgupta S, Bandyopadhyay I, Wakabayashi K. A new cell secreting insulin. Endocrinology 2003; 144:1585-93. [PMID: 12639943 DOI: 10.1210/en.2002-220350] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The pancreatic beta-cell is the only cell in animals that expresses the insulin gene and secretes insulin protein. We have found copious release of immunoreactive and bioactive insulin into the medium from the primary culture of carp adipocytes. Glucose augmented this release to more than 2-fold, and glucose transporter, Glut2, was detected in these cells. These all reflect characteristics of a pancreatic beta-cell. The expression of the adipocyte-specific flotillin gene, the presence of peroxisomal proliferator-activated receptor gamma and Glut4, and the colocalization of insulin and leptin confirmed the identity of these cells as adipocytes. Purified carp adipocyte insulin (AdpInsl) comigrated with porcine and bovine insulin in SDS-PAGE, indicating the similarity of their molecular sizes (5.5 kDa). AdpInsl strongly reduced hyperglycemia in streptozotocin-induced diabetic rats. It also stimulated significantly higher glucose uptake in carp and hamster adipocytes than porcine insulin. Adipocyte RNA hybridized with rat and zebrafish insulin cDNA showing the expression of the insulin gene in this cell. Using oligonucleotide primers designed on the basis of conserved insulin domain, AdpInsl cDNA was reverse transcribed, cloned, and sequenced. The deduced amino acid sequence of AdpInsl A and B chain exhibited 98% homology with zebrafish and more than 70% homology with human, porcine, and murine insulin. To understand the structure-function relationship between AdpInsl and mammalian beta-cell insulin, we have analyzed the amino acid sequences and three-dimensional structure of AdpInsl. In the critical determinant segment for receptor binding, AdpInsl has His at the A8 position instead of Thr in human and porcine insulin, and this attributed greater biological activity to AdpInsl. Our results show that carp adipocyte is a unique cell. As an insulin target cell it can express the insulin gene and secrete highly active insulin protein; thus, it may serve as a natural alternative to pancreatic beta-cell insulin.
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Affiliation(s)
- Sib Sankar Roy
- Indian Institute of Chemical Biology, Calcutta 700032, India
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27
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Chau PL, Howe PWA. Analysis methods for identifying coordinated movements during ligand unbinding. J Comput Aided Mol Des 2002; 16:755-65. [PMID: 12650592 DOI: 10.1023/a:1022475832253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Molecular dynamics simulations have been applied to unbind biological ligands from their receptors. Conformation changes are observed in the biomolecules during unbinding, but there exists no systematic method to detect these conformation changes. In this work, we have used 'essential dynamics' (ED) and projection to latent structures (PLS) to investigate the conformation changes of the bovine serum retinol-binding protein when retinol unbinds from its receptor site. The results of these analyses characterise a large proportion of the movements that occur during unbinding. We find that the loop regions of retinol-binding protein exhibit the largest movements during unbinding. The sudden changes in unbinding speed during the unbinding process appear not to be caused by sudden changes in protein structure.
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Affiliation(s)
- P L Chau
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.
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28
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Walters KJ, Ferentz AE, Hare BJ, Hidalgo P, Jasanoff A, Matsuo H, Wagner G. Characterizing protein-protein complexes and oligomers by nuclear magnetic resonance spectroscopy. Methods Enzymol 2001; 339:238-58. [PMID: 11462814 DOI: 10.1016/s0076-6879(01)39316-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- K J Walters
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
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29
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Shahied L, Braswell EH, LeStourgeon WM, Krezel AM. An antiparallel four-helix bundle orients the high-affinity RNA binding sites in hnRNP C: a mechanism for RNA chaperonin activity. J Mol Biol 2001; 305:817-28. [PMID: 11162094 DOI: 10.1006/jmbi.2000.4331] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous studies have shown that the C protein of 40 S hnRNP complexes contains a leucine-zipper domain, residues 180-207, and that a 40 residue highly basic domain, immediately preceding the zipper, is responsible for almost all of the free energy of RNA binding to C protein. Because this domain arrangement is like that seen in the bZIP transcription factors it has been termed the bZIP-like-motif or bZLM. We report here that the zipper domain drives C protein oligomerization through its spontaneous assembly into an anti-parallel four-helix bundle approximately 50 A in length. The anti-parallel nature of the four-helix bundle positions the tetramer's four high-affinity RNA binding domains at opposing ends of a rigid core formed by the helix bundle. This domain topology is ideally suited to accommodate and direct a double wrapping of RNA around the tetramer and is fully consistent with C protein's ability to bind and order 230 nt lengths of pre-mRNA through a highly cooperative RNA binding mode. We have used a novel sequence-specific 13C/15N labeling strategy and multidimensional NMR spectroscopy to define the anti-parallel orientation of the four-helix bundle and its molecular dimensions. In vitro reconstitution and hydrodynamic studies on native C protein, on several C protein fragments, and on various synthetic peptides, are consistent with the proposed model and indicate that C protein's canonical RNA recognition motifs probably function in tetramer-tetramer interactions during 40 S hnRNP assembly.
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Affiliation(s)
- L Shahied
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235-1634, USA
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