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Mandal PK, Collie GW, Kauffmann B, Huc I. Racemic crystal structures of A-DNA duplexes. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:709-715. [PMID: 35647918 PMCID: PMC9159285 DOI: 10.1107/s2059798322003928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/10/2022] [Indexed: 11/20/2022]
Abstract
Racemic crystallography benefits the identification of a structural form of a DNA sequence that was not previously observed for the enantiopure equivalent. The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.
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2
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Eltareb A, Lopez GE, Giovambattista N. The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine. Phys Chem Chem Phys 2021; 23:19402-19414. [PMID: 34494044 PMCID: PMC8491127 DOI: 10.1039/d1cp02734d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures (T ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water can exist in two amorphous ices at P < 1 GPa, low-density amorphous (LDA) ice at low pressures and high-density amorphous ice (HDA) at high pressures; HDA is ≈20-25% denser than LDA. While fast/plunge cooling at 1 bar brings the sample into LDA, high-pressure cooling (HPC), at sufficiently high pressure, produces HDA. HDA can also be produced by isothermal compression of LDA at cryogenic temperatures. Here, we perform classical molecular dynamics simulations to study the effects of LDA, HDA, and the LDA-HDA transformation on the structure and hydration of a small peptide, polyalanine. We follow thermodynamic paths corresponding to (i) fast/plunge cooling at 1 bar, (ii) HPC at P = 400 MPa, and (iii) compression/decompression cycles at T = 80 K. While process (i) produced LDA in the system, path (iii) produces HDA. Interestingly, the amorphous ice produced in process (ii) is an intermediate amorphous ice (IA) with properties that fall in-between those of LDA and HDA. Remarkably, the structural changes in polyalanine are negligible at all conditions studied (0-2000 MPa, 80-300 K) even when water changes among the low and high-density liquid states as well as the amorphous solids LDA, IA, and HDA. The similarities and differences in the hydration of polyalanine vitrified in LDA, IA, and HDA are described. Since the studied thermodynamic paths are suitable for the cryopreservation of biomolecules, we also study the structure and hydration of polyalanine along isobaric and isochoric heating paths, which can be followed experimentally for the recovery of cryopreserved samples. Upon heating, the structure of polyalanine remains practically unchanged. We conclude with a brief discussion of the practical advantages of (a) using HDA and IA as a cryoprotectant environment (as opposed to LDA), and (b) the use of isochoric heating as a recovery process (as opposed to isobaric heating).
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Affiliation(s)
- Ali Eltareb
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Gustavo E Lopez
- Department of Chemistry, Lehman College of the City University of New York, Bronx, New York 10468, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Nicolas Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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3
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Hu R, Yang G, Ding HM, Ma J, Ma YQ, Gan J, Chen G. Competition between Supramolecular Interaction and Protein–Protein Interaction in Protein Crystallization: Effects of Crystallization Method and Small Molecular Bridge. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | - Hong-ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | | | - Yu-qiang Ma
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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4
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Zhang F, Ma H, Bowatte K, Kwiatkowski D, Mittmann E, Qasem H, Krauß N, Zeng X, Ren Z, Scheerer P, Yang X, Lamparter T. Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Photochem Photobiol 2017; 93:304-314. [DOI: 10.1111/php.12699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Fan Zhang
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
- Institute of Materials; China Academy of Engineering Physics; Mianyang China
| | - Hongju Ma
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Kalinga Bowatte
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Dennis Kwiatkowski
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Esther Mittmann
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Heba Qasem
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Xiaoli Zeng
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Zhong Ren
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Xiaojing Yang
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Tilman Lamparter
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
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5
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Zander U, Bourenkov G, Popov AN, de Sanctis D, Svensson O, McCarthy AA, Round E, Gordeliy V, Mueller-Dieckmann C, Leonard GA. MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2328-43. [PMID: 26527148 PMCID: PMC4631482 DOI: 10.1107/s1399004715017927] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 01/30/2023]
Abstract
Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.
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Affiliation(s)
- Ulrich Zander
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alexander N. Popov
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Daniele de Sanctis
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Olof Svensson
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 38042 Grenoble, France
| | - Ekaterina Round
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Valentin Gordeliy
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- ICS-6: Molecular Biophysics, Institute of Complex Systems (ICS), Research Centre Juelich, 52425 Juelich, Germany
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | | | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble, France
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Pflugrath JW. Practical macromolecular cryocrystallography. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:622-42. [PMID: 26057787 PMCID: PMC4461322 DOI: 10.1107/s2053230x15008304] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022]
Abstract
Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.
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Affiliation(s)
- J W Pflugrath
- Rigaku Americas Corp., 9009 New Trails Drive, The Woodlands, TX 77381, USA
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Thompson MC, Cascio D, Leibly DJ, Yeates TO. An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein. Protein Sci 2015; 24:956-75. [PMID: 25752492 DOI: 10.1002/pro.2672] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/23/2015] [Accepted: 03/03/2015] [Indexed: 01/01/2023]
Abstract
The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095
| | - David J Leibly
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095.,UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095
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8
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Thompson MC, Crowley CS, Kopstein J, Bobik TA, Yeates TO. Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr F Struct Biol Commun 2014; 70:1584-90. [PMID: 25484204 PMCID: PMC4259218 DOI: 10.1107/s2053230x1402158x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/30/2014] [Indexed: 03/10/2023] Open
Abstract
The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein-ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher S. Crowley
- Molecular Biology Interdepartmental PhD Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jeffrey Kopstein
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas A. Bobik
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Interdepartmental PhD Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- UCLA–DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
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9
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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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10
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Protein crystalline frameworks with controllable interpenetration directed by dual supramolecular interactions. Nat Commun 2014; 5:4634. [DOI: 10.1038/ncomms5634] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 07/09/2014] [Indexed: 11/08/2022] Open
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11
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Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:92-100. [PMID: 25117499 DOI: 10.1016/j.pbiomolbio.2014.08.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/23/2014] [Accepted: 08/02/2014] [Indexed: 11/23/2022]
Abstract
X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility.
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12
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Bruździak P, Panuszko A, Stangret J. Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization. J Phys Chem B 2013; 117:11502-8. [DOI: 10.1021/jp404780c] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Bruździak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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13
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Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. Proc Natl Acad Sci U S A 2013; 110:7217-22. [PMID: 23589886 DOI: 10.1073/pnas.1302377110] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 Å resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family.
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Abstract
Proteins are marginally stable, and the folding/unfolding equilibrium of proteins in aqueous solution can easily be altered by the addition of small organic molecules known as cosolvents. Cosolvents that shift the equilibrium toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the molecular mechanism of its action has been vigorously debated in the literature. Here we review recent experimental as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the molecular mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed molecular simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.
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Affiliation(s)
- Deepak R Canchi
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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15
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Kim CU, Wierman JL, Gillilan R, Lima E, Gruner SM. A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter. J Appl Crystallogr 2012; 46:234-241. [PMID: 23396891 DOI: 10.1107/s0021889812045013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/30/2012] [Indexed: 11/11/2022] Open
Abstract
High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydrated via vapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryo-cooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.
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Affiliation(s)
- Chae Un Kim
- Cornell High Energy Synchrotron Source (CHESS) and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
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16
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Bruździak P, Rakowska PW, Stangret J. Chemometric method of spectra analysis leading to isolation of lysozyme and CtDNA spectra affected by osmolytes. APPLIED SPECTROSCOPY 2012; 66:1302-1310. [PMID: 23146186 DOI: 10.1366/11-06581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this paper we present a chemometric method of analysis leading to isolation of Fourier transform infrared (FT-IR) spectra of biomacromolecules (HEW lysozyme, ctDNA) affected by osmolytes (trimethylamine-N-oxide and N,N,N-trimethylglycine, respectively) in aqueous solutions. The method is based on the difference spectra method primarily used to characterize the structure of solvent affected by solute. The cyclical usage of factor analysis allows precise information to be obtained on the shape of "affected spectra" of analyzed biomacromolecules. "Affected spectra" of selected biomacromolecules give valuable information on their structure in the presence of the osmolytes in solution, as well as on the level of perturbation in dependence of osmolyte concentration. The method also gives a possibility of insight into the mechanism of interaction in presented types of systems. It can be easily adapted to various chemical and biochemical problems where vibrational or ultraviolet-visible (UV-Vis) spectroscopy is used.
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Affiliation(s)
- Piotr Bruździak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Poland.
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17
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von Stetten D, Batot GO, Noirclerc-Savoye M, Royant A. Alteration of fluorescent protein spectroscopic properties upon cryoprotection. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1578-83. [DOI: 10.1107/s0907444912037900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/04/2012] [Indexed: 05/26/2023]
Abstract
Cryoprotection of a protein crystal by addition of small-molecule compounds may sometimes affect the structure of its active site. The spectroscopic and structural effects of the two cryoprotectants glycerol and ethylene glycol on the cyan fluorescent protein Cerulean were investigated. While glycerol had almost no noticeable effect, ethylene glycol was shown to induce a systematic red shift of the UV–vis absorption and fluorescence emission spectra. Additionally, ethylene glycol molecules were shown to enter the core of the protein, with one of them binding in close vicinity to the chromophore, which provides a sound explanation for the observed spectroscopic changes. These results highlight the need to systematically record spectroscopic data on crystals of light-absorbing proteins and reinforce the notion that fluorescent proteins must not been seen as rigid structures.
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Canchi DR, Jayasimha P, Rau DC, Makhatadze GI, Garcia AE. Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. J Phys Chem B 2012; 116:12095-104. [PMID: 22970901 DOI: 10.1021/jp304298c] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a naturally occurring protecting osmolyte that stabilizes the folded state of proteins and also counteracts the destabilizing effect of urea on protein stability. Experimentally, it has been inferred that TMAO is preferentially excluded from the vicinity of protein surfaces. Here, we combine computer modeling and experimental measurements to gain an understanding of the mechanism of the protecting effect of TMAO on proteins. We have developed an all-atom molecular model for TMAO that captures the exclusion of TMAO from model compounds and protein surfaces, as a consequence of incorporating realistic TMAO-water interactions through osmotic pressure measurements. Osmotic pressure measurements also suggest no significant attraction between urea and TMAO molecules in solution. To obtain an accurate potential for molecular simulations of protein stability in TMAO solutions, we have explored different ways of parametrizing the protein/osmolyte and osmolyte/osmolyte interactions by scaling charges and the strength of Lennard-Jones interactions and carried out equilibrium folding experiments of Trp-cage miniprotein in the presence of TMAO to guide the parametrization. Our calculations suggest a general principle for preferential interaction behavior of cosolvents with protein surfaces--preferentially excluded osmolytes have repulsive self-interaction given by osmotic coefficient φ > 1, while denaturants, in addition to having attractive interactions with the proteins, have favorable self-interaction given by osmotic coefficient φ < 1, to enable preferential accumulation in the vicinity of proteins.
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Affiliation(s)
- Deepak R Canchi
- Department of Chemical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Pemberton TA, Still BR, Christensen EM, Singh H, Srivastava D, Tanner JJ. Proline: Mother Nature's cryoprotectant applied to protein crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1010-8. [PMID: 22868767 PMCID: PMC3413213 DOI: 10.1107/s0907444912019580] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/01/2012] [Indexed: 11/10/2022]
Abstract
L-Proline is one of Mother Nature's cryoprotectants. Plants and yeast accumulate proline under freeze-induced stress and the use of proline in the cryopreservation of biological samples is well established. Here, it is shown that L-proline is also a useful cryoprotectant for protein crystallography. Proline was used to prepare crystals of lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase for low-temperature data collection. The crystallization solutions in these test cases included the commonly used precipitants ammonium sulfate, sodium chloride and polyethylene glycol and spanned the pH range 4.6-8.5. Thus, proline is compatible with typical protein-crystallization formulations. The proline concentration needed for cryoprotection of these crystals is in the range 2.0-3.0 M. Complete data sets were collected from the proline-protected crystals. Proline performed as well as traditional cryoprotectants based on the diffraction resolution and data-quality statistics. The structures were refined to assess the binding of proline to these proteins. As observed with traditional cryoprotectants such as glycerol and ethylene glycol, the electron-density maps clearly showed the presence of proline molecules bound to the protein. In two cases, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase, proline binds in the active site. It is concluded that L-proline is an effective cryoprotectant for protein crystallography.
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Affiliation(s)
- Travis A. Pemberton
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Brady R. Still
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Emily M. Christensen
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Dhiraj Srivastava
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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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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