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Hexnerová R, Křížková K, Fábry M, Sieglová I, Kedrová K, Collinsová M, Ullrichová P, Srb P, Williams C, Crump MP, Tošner Z, Jiráček J, Veverka V, Žáková L. Probing Receptor Specificity by Sampling the Conformational Space of the Insulin-like Growth Factor II C-domain. J Biol Chem 2016; 291:21234-21245. [PMID: 27510031 PMCID: PMC5076530 DOI: 10.1074/jbc.m116.741041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 01/22/2023] Open
Abstract
Insulin and insulin-like growth factors I and II are closely related protein hormones. Their distinct evolution has resulted in different yet overlapping biological functions with insulin becoming a key regulator of metabolism, whereas insulin-like growth factors (IGF)-I/II are major growth factors. Insulin and IGFs cross-bind with different affinities to closely related insulin receptor isoforms A and B (IR-A and IR-B) and insulin-like growth factor type I receptor (IGF-1R). Identification of structural determinants in IGFs and insulin that trigger their specific signaling pathways is of increasing importance in designing receptor-specific analogs with potential therapeutic applications. Here, we developed a straightforward protocol for production of recombinant IGF-II and prepared six IGF-II analogs with IGF-I-like mutations. All modified molecules exhibit significantly reduced affinity toward IR-A, particularly the analogs with a Pro-Gln insertion in the C-domain. Moreover, one of the analogs has enhanced binding affinity for IGF-1R due to a synergistic effect of the Pro-Gln insertion and S29N point mutation. Consequently, this analog has almost a 10-fold higher IGF-1R/IR-A binding specificity in comparison with native IGF-II. The established IGF-II purification protocol allowed for cost-effective isotope labeling required for a detailed NMR structural characterization of IGF-II analogs that revealed a link between the altered binding behavior of selected analogs and conformational rearrangement of their C-domains.
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Affiliation(s)
- Rozálie Hexnerová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Květoslava Křížková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Milan Fábry
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic, and
| | - Irena Sieglová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Kateřina Kedrová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic, Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Michaela Collinsová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Pavlína Ullrichová
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - Pavel Srb
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Christopher Williams
- Department of Organic and Biological Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Matthew P Crump
- Department of Organic and Biological Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Zdeněk Tošner
- Faculty of Science, Charles University in Prague, Albertov 6, Prague 128 43, Czech Republic
| | - Jiří Jiráček
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic,
| | - Lenka Žáková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám 2, 166 10 Prague 6, Czech Republic,
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2
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Roedig P, Duman R, Sanchez-Weatherby J, Vartiainen I, Burkhardt A, Warmer M, David C, Wagner A, Meents A. Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering. J Appl Crystallogr 2016; 49:968-975. [PMID: 27275143 PMCID: PMC4886986 DOI: 10.1107/s1600576716006348] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/14/2016] [Indexed: 11/25/2022] Open
Abstract
Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.
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Affiliation(s)
- Philip Roedig
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Ramona Duman
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | | | - Anja Burkhardt
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Martin Warmer
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | | | - Armin Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
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3
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Huang CY, Olieric V, Ma P, Howe N, Vogeley L, Liu X, Warshamanage R, Weinert T, Panepucci E, Kobilka B, Diederichs K, Wang M, Caffrey M. In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Acta Crystallogr D Struct Biol 2016; 72:93-112. [PMID: 26894538 PMCID: PMC4756617 DOI: 10.1107/s2059798315021683] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/15/2015] [Indexed: 11/21/2022] Open
Abstract
Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introduced in meso in situ serial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, α-helical and β-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.
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Affiliation(s)
- Chia-Ying Huang
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Pikyee Ma
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
- Laboratory of Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Nicole Howe
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Lutz Vogeley
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
| | - Xiangyu Liu
- School of Medicine, Tsinghua University, Beijing 100084, People’s Republic of China
| | | | - Tobias Weinert
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Brian Kobilka
- School of Medicine, Tsinghua University, Beijing 100084, People’s Republic of China
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz, Germany
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland
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Farley C, Juers DH. Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols. J Struct Biol 2014; 188:102-6. [PMID: 25286441 DOI: 10.1016/j.jsb.2014.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/14/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
Abstract
Macromolecular X-ray crystallography, usually done at cryogenic temperature to limit radiation damage, often requires liquid cryoprotective soaking that can be labor intensive and damaging to crystals. Here we describe a method for cryoprotection that uses vapor diffusion of volatile cryoprotective agents into loop-mounted crystals. The crystal is mounted into a vial containing a small volume of an alcohol-based cryosolution. After a short incubation with the looped crystal sitting in the cryosolution vapor, the crystal is transferred directly from the vial into the cooling medium. Effective for several different protein crystals, the approach obviates the need for liquid soaking and opens up a heretofore underutilized class of cryoprotective agents for macromolecular crystallography.
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Affiliation(s)
- Christopher Farley
- Department of Physics, Whitman College, Walla Walla, WA 99362, United States
| | - Douglas H Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, United States; Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, WA 99362, United States.
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5
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Bagchi K, Roy S. Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions. J Phys Chem B 2014; 118:3805-13. [DOI: 10.1021/jp411136w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kushal Bagchi
- St. Joseph’s College for Arts and Science, Bangalore 560027, India
| | - Susmita Roy
- SSCU, Indian Institute of Science, Bangalore 560012, India
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6
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Baba S, Hoshino T, Ito L, Kumasaka T. Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1839-49. [PMID: 23999307 PMCID: PMC3760132 DOI: 10.1107/s0907444913018027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/29/2013] [Indexed: 11/11/2022]
Abstract
Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection.
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Affiliation(s)
- Seiki Baba
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takeshi Hoshino
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Len Ito
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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7
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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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Burkhardt A, Warmer M, Panneerselvam S, Wagner A, Zouni A, Glöckner C, Reimer R, Hohenberg H, Meents A. Fast high-pressure freezing of protein crystals in their mother liquor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:495-500. [PMID: 22505429 PMCID: PMC3325829 DOI: 10.1107/s1744309112009670] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/05/2012] [Indexed: 01/09/2023]
Abstract
High-pressure freezing (HPF) is a method which allows sample vitrification without cryoprotectants. In the present work, protein crystals were cooled to cryogenic temperatures at a pressure of 210 MPa. In contrast to other HPF methods published to date in the field of cryocrystallography, this protocol involves rapid sample cooling using a standard HPF device. The fast cooling rates allow HPF of protein crystals directly in their mother liquor without the need for cryoprotectants or external reagents. HPF was first attempted with hen egg-white lysozyme and cubic insulin crystals, yielding good to excellent diffraction quality. Non-cryoprotected crystals of the membrane protein photosystem II have been successfully cryocooled for the first time. This indicates that the presented HPF method is well suited to the vitrification of challenging systems with large unit cells and weak crystal contacts.
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Affiliation(s)
- Anja Burkhardt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.
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9
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Shao Q, Fan Y, Yang L, Qin Gao Y. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 2012; 136:115101. [DOI: 10.1063/1.3692801] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Tao Y, Julian RR. Examining protein surface structure in highly conserved sequence variants with mass spectrometry. Biochemistry 2012; 51:1796-802. [PMID: 22320248 DOI: 10.1021/bi2018199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins.
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Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California, Riverside, California 92521, United States
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11
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Marshall H, Venkat M, Hti Lar Seng NS, Cahn J, Juers DH. The use of trimethylamine N-oxide as a primary precipitating agent and related methylamine osmolytes as cryoprotective agents for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:69-81. [PMID: 22194335 PMCID: PMC3245723 DOI: 10.1107/s0907444911050360] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/23/2011] [Indexed: 11/10/2022]
Abstract
Both crystallization and cryoprotection are often bottlenecks for high-resolution X-ray structure determination of macromolecules. Methylamine osmolytes are known stabilizers of protein structure. One such osmolyte, trimethylamine N-oxide (TMAO), has seen occasional use as an additive to improve macromolecular crystal quality and has recently been shown to be an effective cryoprotective agent for low-temperature data collection. Here, TMAO and the related osmolytes sarcosine and betaine are investigated as primary precipitating agents for protein crystal growth. Crystallization experiments were undertaken with 14 proteins. Using TMAO, seven proteins crystallized in a total of 13 crystal forms, including a new tetragonal crystal form of trypsin. The crystals diffracted well, and eight of the 13 crystal forms could be effectively cryocooled as grown with TMAO as an in situ cryoprotective agent. Sarcosine and betaine produced crystals of four and two of the 14 proteins, respectively. In addition to TMAO, sarcosine and betaine were effective post-crystallization cryoprotective agents for two different crystal forms of thermolysin. Precipitation reactions of TMAO with several transition-metal ions (Fe(3+), Co(2+), Cu(2+) and Zn(2+)) did not occur with sarcosine or betaine and were inhibited for TMAO at lower pH. Structures of proteins from TMAO-grown crystals and from crystals soaked in TMAO, sarcosine or betaine were determined, showing osmolyte binding in five of the 12 crystals tested. When an osmolyte was shown to bind, it did so near the protein surface, interacting with water molecules, side chains and backbone atoms, often at crystal contacts.
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Affiliation(s)
- Haley Marshall
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, Washington, USA
| | - Murugappan Venkat
- Department of Physics, Whitman College, Walla Walla, Washington, USA
| | - Nang San Hti Lar Seng
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, Washington, USA
| | - Jackson Cahn
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, Washington, USA
| | - Douglas H. Juers
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, Washington, USA
- Department of Physics, Whitman College, Walla Walla, Washington, USA
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12
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Muzaffar M, Ahmad A. The mechanism of enhanced insulin amyloid fibril formation by NaCl is better explained by a conformational change model. PLoS One 2011; 6:e27906. [PMID: 22132167 PMCID: PMC3221682 DOI: 10.1371/journal.pone.0027906] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/27/2011] [Indexed: 01/05/2023] Open
Abstract
The high propensity of insulin to fibrillate causes severe biomedical and biotechnological complications. Insulin fibrillation studies attain significant importance considering the prevalence of diabetes and the requirement of functional insulin in each dose. Although studied since the early years of the 20(th) century, elucidation of the mechanism of insulin fibrillation has not been understood completely. We have previously, through several studies, shown that insulin hexamer dissociates into monomer that undergoes partial unfolding before converting into mature fibrils. In this study we have established that NaCl enhances insulin fibrillation mainly due to subtle structural changes and is not a mere salt effect. We have carried out studies both in the presence and absence of urea and Gdn.HCl and compared the relationship between conformation of insulin induced by urea and Gdn.HCl with respect to NaCl at both pH 7.4 (hexamer) and pH 2 (monomer). Fibril formation was followed with a Thioflavin T assay and structural changes were monitored by circular dichroism and size-exclusion chromatography. The results show salt-insulin interactions are difficult to classify as commonly accepted Debye-Hückel or Hofmeister series interactions but instead a strong correlation between the association states and conformational states of insulin and their propensity to fibrillate is evident.
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Affiliation(s)
- Mahvish Muzaffar
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
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13
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Liu ZJ, Chen L, Wu D, Ding W, Zhang H, Zhou W, Fu ZQ, Wang BC. A multi-dataset data-collection strategy produces better diffraction data. Acta Crystallogr A 2011; 67:544-9. [PMID: 22011470 PMCID: PMC3211246 DOI: 10.1107/s0108767311037469] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/14/2011] [Indexed: 11/27/2022] Open
Abstract
A multi-dataset (MDS) data-collection strategy is proposed and analyzed for macromolecular crystal diffraction data acquisition. The theoretical analysis indicated that the MDS strategy can reduce the standard deviation (background noise) of diffraction data compared with the commonly used single-dataset strategy for a fixed X-ray dose. In order to validate the hypothesis experimentally, a data-quality evaluation process, termed a readiness test of the X-ray data-collection system, was developed. The anomalous signals of sulfur atoms in zinc-free insulin crystals were used as the probe to differentiate the quality of data collected using different data-collection strategies. The data-collection results using home-laboratory-based rotating-anode X-ray and synchrotron X-ray systems indicate that the diffraction data collected with the MDS strategy contain more accurate anomalous signals from sulfur atoms than the data collected with a regular data-collection strategy. In addition, the MDS strategy offered more advantages with respect to radiation-damage-sensitive crystals and better usage of rotating-anode as well as synchrotron X-rays.
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Affiliation(s)
- Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hua Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Weihong Zhou
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Grochulski P, Fodje MN, Gorin J, Labiuk SL, Berg R. Beamline 08ID-1, the prime beamline of the Canadian Macromolecular Crystallography Facility. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:681-684. [PMID: 21685687 DOI: 10.1107/s0909049511019431] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
Beamline 08ID-1 is the prime macromolecular crystallography beamline at the Canadian Light Source. Based on a small-gap in-vacuum undulator, it is designed for challenging projects like small crystals and crystals with large cell dimensions. Beamline 08ID-1, together with a second bending-magnet beamline, constitute the Canadian Macromolecular Crystallography Facility (CMCF). This paper presents an overall description of the 08ID-1 beamline, including its specifications, beamline software and recent scientific highlights. The end-station of the beamline is equipped with a CCD X-ray detector, on-axis crystal visualization system, a single-axis goniometer and a sample automounter allowing remote access to the beamline. The general user program is guaranteed up to 55% of the useful beam time and is run under a peer-review proposal system. The CMCF staff provide `Mail-in' crystallography service to the users with the highest-scored proposals.
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Affiliation(s)
- Pawel Grochulski
- Canadian Light Source Inc., 101 Perimeter Road, Saskatoon, Saskatchewan, Canada
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15
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Howard-Jones AR, Adam V, Cowley A, Baldwin JE, Bourgeois D. Cryophotolysis of a caged oxygen compound for use in low temperature biological studies. Photochem Photobiol Sci 2009; 8:1150-6. [PMID: 19639117 DOI: 10.1039/b821516b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanistic investigations of biological enzymatic processes require controlled initiation and monitoring of catalytic reactions. A well-known technique to trap and observe reaction intermediates building up along a reaction pathway is the use of low temperature conditions. Here, we report a kinetically competent system for the release of molecular oxygen at cryogenic temperature, using a cobalt-based caged oxygen molecule, (micro-peroxo)(micro-hydroxo)bis[bis(bipyridyl)cobalt(III)] nitrate. Cryophotolysis of this compound was induced using 266 nm laser light and monitored by absorption microspectrophotometry. Furthermore, to verify that photo-fragmentation was accompanied by release of the active caged molecule, the production of dioxygen during cryophotolysis was directly visualized. This work lays the foundations for the use of low temperature reaction triggering as a tool to prolong the lifetime of normally unstable intermediate states in oxygen-dependent enzymes.
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16
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Sreekanth R, Pattabhi V, Rajan S. Metal induced structural changes observed in hexameric insulin. Int J Biol Macromol 2009; 44:29-36. [DOI: 10.1016/j.ijbiomac.2008.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/19/2008] [Accepted: 09/19/2008] [Indexed: 11/24/2022]
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17
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Niimura N, Bau R. Neutron protein crystallography: beyond the folding structure of biological macromolecules. Acta Crystallogr A 2007; 64:12-22. [DOI: 10.1107/s0108767307043498] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 09/05/2007] [Indexed: 11/10/2022] Open
Abstract
Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.
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18
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Forsythe E, Achari A, Pusey ML. Trace fluorescent labeling for high-throughput crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2006; 62:339-46. [PMID: 16510981 PMCID: PMC1409766 DOI: 10.1107/s0907444906000813] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 01/06/2006] [Indexed: 11/10/2022]
Abstract
Covalent labeling of macromolecules with trace levels (<1%) of a fluorescent dye is proposed as a means to facilitate finding or detecting crystals in crystallization drops. To test the effects of labeled protein concentration on the resulting X-ray diffraction data, experiments were carried out with the model proteins insulin, ribonuclease, lysozyme and thaumatin, which were labeled with the fluorescent dye carboxyrhodamine. All proteins were labeled on their N-terminal amine and lysozyme was also labeled randomly on lysine side chains in a separate series of experiments. Ribonuclease and N-terminal amine-labeled lysozyme crystals were poorly formed at 10% label concentration and these were not used in subsequent diffraction experiments. All model proteins were tested to 5% labeled protein, and thaumatin and randomly labeled lysozyme gave well formed crystals to 10% labeled protein. In all cases tested, the presence of the label was found to not significantly affect the X-ray diffraction data quality obtained. Qualitative visual-inspection experiments over a range of label concentrations indicated that optimum derivatization levels ranged from 0.025-0.05% for insulin to 0.1-0.25% for thaumatin. Light intensity is a simpler search parameter than straight lines and by virtue of being the most densely packed phase, labeled crystals should be the most intense light sources under fluorescent illumination. For both visual and automated methods of crystal detection, label intensity is a simpler and potentially more powerful search parameter. Screening experiments using the proteins canavalin, beta-lactoglobulins A and B and chymotrypsinogen, all at 0.5% label concentration, demonstrated the utility of this approach to rapidly finding crystals, even when obscured by precipitate. The use of trace-labeled protein is also proposed to be useful for the automated centering of crystals in X-ray beamlines.
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Moulaei T, Maehigashi T, Lountos GT, Komeda S, Watkins D, Stone MP, Marky LA, Li JS, Gold B, Williams LD. Structure of B-DNA with cations tethered in the major groove. Biochemistry 2005; 44:7458-68. [PMID: 15895989 DOI: 10.1021/bi050128z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we describe the 1.6-A X-ray structure of the DDD (Dickerson-Drew dodecamer), which has been covalently modified by the tethering of four cationic charges. This modified version of the DDD, called here the DDD(4+), is composed of [d(CGCGAAXXCGCG)](2), where X is effectively a thymine residue linked at the 5 position to an n-propyl-amine. The structure was determined from crystals soaked with thallium(I), which has been broadly used as a mimic of K(+) in X-ray diffraction experiments aimed at determining positions of cations adjacent to nucleic acids. Three of the tethered cations are directed radially out from the DNA. The radially directed tethered cations do not appear to induce structural changes or to displace counterions. One of the tethered cations is directed in the 3' direction, toward a phosphate group near one end of the duplex. This tethered cation appears to interact electrostatically with the DNA. This interaction is accompanied by changes in helical parameters rise, roll, and twist and by a displacement of the backbone relative to a control oligonucleotide. In addition, these interactions appear to be associated with displacement of counterions from the major groove of the DNA.
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Affiliation(s)
- Tinoush Moulaei
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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20
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Guinto ER, Di Cera E. Large heat capacity change in a protein-monovalent cation interaction. Biochemistry 1996; 35:8800-4. [PMID: 8688415 DOI: 10.1021/bi9608828] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Current views about protein-ligand interactions state that electrostatic forces drive the binding of charged species and that burial of hydrophobic and polar surfaces controls the heat capacity change associated with the reaction. For the interaction of a protein with a monovalent cation the electrostatic components are expected to be significant due to the ionic nature of the ligand, whereas the heat capacity change is expected to be small due to the size of the surface area involved in the recognition event. The physiologically important interaction of Na+ with thrombin was studied over the temperature range from 5 to 45 degrees C and the ionic strength range from 50 to 800 mM. These measurements reveal an unanticipated result that bears quite generally on studies of molecular recognition and protein folding. Binding of Na+ to thrombin is characterized by a modest dependence on ionic strength but a large and negative heat capacity change of -1.1 +/- 0.1 kcal mol-1 K-1. The small electrostatic coupling can be explained in terms of a minimal perturbation of the ionic atmosphere of the protein upon Na+ binding. The large heat capacity change, however, is difficult to reconcile with current views on the origin of this effect from surface area changes or large folding transitions coupled to binding. It is proposed that this change is linked to burial of a large cluster of water molecules in the Na+ binding pocket upon Na+ binding. Due to their reduced mobility and highly ordered structure, water molecules sequestered in the interior of a protein must have a lower heat capacity compared to those on the surface of a protein or in the bulk solvent. Hence, a binding or folding event where water molecules are buried may result in significant heat capacity changes independent of changes in exposed hydrophobic surface or coupled conformational transitions.
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Affiliation(s)
- E R Guinto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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21
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Abstract
Packing contacts are crystal artifacts, yet they make use of the same forces that govern specific recognition in protein-protein complexes and oligomeric proteins. They provide examples of a nonspecific protein-protein interaction which can be compared to biologically relevant ones. We evaluate the number and size of pairwise interfaces in 152 crystal forms where the asymmetric unit contains a monomeric protein. In those crystal forms that have no element of 2-fold symmetry, we find that molecules form 8 to 10 pairwise interfaces. The total area of the surface buried on each molecule is large, up to 4400 A2. Pairwise interfaces bury 200-1200 A2, like interfaces generated at random in a computer simulation, and less than interfaces in protease-inhibitor or antigen-antibody complexes, which bury 1500 A2 or more. Thus, specific contacts occurring in such complexes extend over a larger surface than nonspecific ones. In crystal forms with 2-fold symmetry, pairwise interfaces are fewer and larger on average than in the absence of 2-fold symmetry. Some bury 1500-2500 A2, like interfaces in oligomeric proteins, and create "crystal oligomers" which may have formed in the solution before crystallizing.
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Affiliation(s)
- J Janin
- Laboratoire de Biologie Structurale, CNRS-Université Paris-Sud, Gif-sur-Yvette, France
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23
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Peracchi A, Mozzarelli A, Rossi GL. Monovalent cations affect dynamic and functional properties of the tryptophan synthase alpha 2 beta 2 complex. Biochemistry 1995; 34:9459-65. [PMID: 7626616 DOI: 10.1021/bi00029a022] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Monovalent cations affect both conformational and catalytic properties of the tryptophan synthase alpha 2 beta 2 complex from Salmonella typhimurium. Their influence on the dynamic properties of the enzyme was probed by monitoring the phosphorescence decay of the unique Trp-177 beta, a residue located near the beta-active site, at the interface between alpha- and beta-subunits. In the presence of either Li+, Na+, Cs+, or NH4+, the phosphorescence decay is biphasic and the average lifetime increases indicating a decrease in the flexibility of the N-terminal domain of the beta-subunit. Since amplitudes but not lifetimes are affected, cations appear to shift the equilibrium between preexisting enzyme conformations. The effect on the reaction between indole and L-serine was studied by steady state kinetic methods at room temperature. We found that cations: (i) bind to the L-serine--enzyme derivatives with an apparent dissociation constant, measured as the concentration of cation corresponding to one-half of the maximal activity, that is in the millimolar range and decreases with ion size; (ii) increase kcat with the order of efficacy Cs+ > K+ > Li+ > Na+; (iii) decrease KM for indole, Na+ being the most effective and causing a 30-fold decrease; and (iv) cause an increase of the kcat/KM ratio by 20-40-fold. The influence on the equilibrium distribution between the external aldimine and the alpha-aminoacrylate, intermediates in the reaction of L-serine with the beta-subunits of the enzyme, was found to be cation-specific.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A Peracchi
- Istituto di Scienze Biochimiche, Università di Parma, Italy
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24
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Gursky O, Fontano E, Bhyravbhatla B, Caspar DL. Stereospecific dihaloalkane binding in a pH-sensitive cavity in cubic insulin crystals. Proc Natl Acad Sci U S A 1994; 91:12388-92. [PMID: 7809046 PMCID: PMC45443 DOI: 10.1073/pnas.91.26.12388] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Crystallographic analysis at 2-A resolution of the selective binding of dihalogenated methane, ethane, and ethylene compounds in the cavity on the cubic insulin dimer axis provides a model for anesthetic-protein interactions. At pH 6-11, 1,2-dichloroethane binds isomorphically in the right-handed cis-conformation, displacing four water molecules from the invariant cavity. Lowering the pH to 5.7 in 1 M Na2SO4 without dihaloalkanes induces a cooperative structural transition in which the dyad cavities between B13 glutamate pairs are constricted, and SO4(2-) ions are bound by rearranged triads of B1 NH+3 groups. In the presence of dichloroethane at pH 5-5.5, the equilibrium is shifted to a mixture of the ligand-bound and ligand-excluding cavity structures, with half-occupancy of the sulfate sites, exemplifying how a volatile anesthetic can act as an allosteric effector. Measurements at pH 9 of the occupancies of structurally similar dihaloalkanes demonstrate a high degree of binding selectivity. Induced polarization of the ligand and bound water by the charge distribution in the binding cavity apparently provides the selective electrostatic interactions that discriminate between dihaloalkanes of comparable size and polarity.
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Affiliation(s)
- O Gursky
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9110
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25
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Badger J, Li Y, Caspar DL. Thallium counterion distribution in cubic insulin crystals determined from anomalous x-ray diffraction data. Proc Natl Acad Sci U S A 1994; 91:1224-8. [PMID: 8108391 PMCID: PMC43129 DOI: 10.1073/pnas.91.4.1224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To determine the distribution of monovalent cations around a protein we have measured anomalous scattering diffraction data from Tl-containing cubic insulin crystals at pH 8 and pH 10.5. The differences between Bijvoet reflection pairs within each set of data were used to calculate anomalous scattering difference maps. Both maps show the same six Tl+ sites, which include two well-ordered Tl+ ions previously identified from isomorphous exchange experiments. The other four sites constitute a second class of cations, which, while much more mobile than the protein atoms, are associated with particular ligating groups. Three of the six Tl+ sites are created exclusively by protein main and side chain carbonyl dipoles rather than negatively charged groups. All of the Tl+ ions are positioned so as to interact with both protein atoms and water molecules. The Tl+ occupancies appear to depend in a complex way on interactions with each other and flexibility in the protein structure. The combined occupancies of these cations are slightly less than is required to neutralize the net protein charge of approximately -2e at pH 8 but account for only about half of the approximately -5e protein charge at pH 10.5. Thus, more disordered counterions, not seen in these Bijvoet anomalous scattering difference maps, are more numerous at higher protein net charge.
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Affiliation(s)
- J Badger
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9110
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26
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Badger J, Kapulsky A, Gursky O, Bhyravbhatla B, Caspar DL. Structure and selectivity of a monovalent cation binding site in cubic insulin crystals. Biophys J 1994; 66:286-92. [PMID: 8161680 PMCID: PMC1275693 DOI: 10.1016/s0006-3495(94)80795-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cubic insulin crystals contain a binding site for monovalent cations in a cavity of the crystal dyad in which the bound cation is ligated by protein atomic dipoles and water molecules. These types of interaction are analogous to interactions that occur in small cation-selective carrier and channel molecules. X-ray diffraction data collected from cubic insulin crystals containing Li+, Na+, K+, NH4+, Rb+, and Tl+ show that (i) the differences in cation size do not cause any large alteration in the protein structure around the cation, and (ii) the bound cation is co-ordinated by one or two water molecules, depending on its ionic radii. The relative binding affinities for cations at this dyad site were obtained from an x-ray diffraction analysis of competition experiments in which crystals were dialyzed in mixtures of Tl+ with Li+, Na+, NH4+, Rb+, or Cs+. These data show that this site provides very little discrimination between Na+, K+, Rb+, and Tl+, some selectivity against the small Li+ and the tetrahedrally shaped NH4+, and stronger selectivity against the larger Cs+. The capacity of this site to bind monovalent cations of different sizes may be accounted for by the small number of protein ligating groups and a change from two ligating waters with Li+ and Na+ to one ligating water with the larger cations.
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Affiliation(s)
- J Badger
- Rosensteil Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254
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27
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Badger J. Display and interpretation of solvent electron density distributions in insulin crystals. JOURNAL OF MOLECULAR GRAPHICS 1993; 11:218-21, 233. [PMID: 8136324 DOI: 10.1016/0263-7855(93)80001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In macromolecular crystallography, three-dimensional contour surfaces are useful for interactive computer graphics displays of the protein electron density but are less effective for presenting static images of large volumes of solvent density. A raster-based computer graphics program which displays depth-cued projections of continuous density distributions has been developed to analyze the distribution of solvent atoms in macromolecular crystals. Maps of the water distribution in the cubic insulin crystal show some well-ordered waters, which are bound to surrounding protein atoms by multiple hydrogen bonds, and an ill-defined solvent structure at a greater distance from the protein surface. Molecular dynamics calculations were used to assist in the interpretation of the time-varying solvent structure within two enclosed cavities in the crystal. Two water molecules that ligate a sodium ion were almost immobile during the stimulation but the majority of water molecules were found to move rapidly between the density maxima identified from the crystallographic refinement.
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Affiliation(s)
- J Badger
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA
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28
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Abstract
Cubic insulin crystals contain approximately 30-A-diameter channels filled with aqueous solvent, providing a useful system in which to analyze hydration structure at a variety of distances from protein surfaces. Beginning with an atomic model for the protein and ordered water molecules, the density distribution in the solvent volume of the phasing model was iteratively refined to improve the fit of calculated structure factors with x-ray diffraction data. The free R value, which compares calculated structure factors with a subset of observed structure factors deliberately omitted from the refinement, was used to provide an objective confirmation of the effectiveness of the refinement procedure. Electron density maps of the solvent, computed using the solvent-refined phases and complete low-resolution diffraction data, reveal multiple hydration layers around the protein.
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Affiliation(s)
- J Badger
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254
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29
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Toney MD, Hohenester E, Cowan SW, Jansonius JN. Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites. Science 1993; 261:756-9. [PMID: 8342040 DOI: 10.1126/science.8342040] [Citation(s) in RCA: 161] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.
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Affiliation(s)
- M D Toney
- Department of Structural Biology, University of Basel, Switzerland
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30
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Gursky O, Badger J, Li Y, Caspar DL. Conformational changes in cubic insulin crystals in the pH range 7-11. Biophys J 1992; 63:1210-20. [PMID: 1477273 PMCID: PMC1261424 DOI: 10.1016/s0006-3495(92)81697-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To determine the effect of variations in the charge distribution on the conformation of a protein molecule, we have solved the structures of bovine cubic insulin over a pH range from 7 to 11 in 0.1 M and 1 M sodium salt solutions. The x-ray data were collected beyond 2-A resolution and the R factors for the refined models ranged from 0.16 to 0.20. Whereas the positions of most protein and well-ordered solvent atoms are conserved, about 30% of residues alter their predominant conformation as the pH is changed. Conformational switching of A5 Gln and B10 His correlates with the pH dependence of monovalent cation binding to insulin in cubic crystals. Shifts in the relative positions of the A chain NH2-terminal and B chain COOH-terminal groups are probably due to titration of the A1 alpha-amino group. Two alternative positions of B25 Phe and A21 Asn observed in cubic insulin at pH 11 are similar to those found in two independent molecules of the 2Zn insulin dimer at pH 6.4. The conformational changes of the insulin amino acids appear to be only loosely coupled at distant protein sites. Shifts in the equilibrium between distinct conformational substates as the charge distribution on the protein is altered are analogous to the electrostatically triggered movements that occur in many functional protein reactions.
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Affiliation(s)
- O Gursky
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110
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