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Li L, Ismagilov RF. Protein crystallization using microfluidic technologies based on valves, droplets, and SlipChip. Annu Rev Biophys 2010; 39:139-58. [PMID: 20192773 DOI: 10.1146/annurev.biophys.050708.133630] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To obtain protein crystals, researchers must search for conditions in multidimensional chemical space. Empirically, thousands of crystallization experiments are carried out to screen various precipitants at multiple concentrations. Microfluidics can manipulate fluids on a nanoliter scale, and it affects crystallization twofold. First, it miniaturizes the experiments that can currently be done on a larger scale and enables crystallization of proteins that are available only in small amounts. Second, it offers unique experimental approaches that are difficult or impossible to implement on a larger scale. Ongoing development of microfluidic techniques and their integration with protein production, characterization, and in situ diffraction promises to accelerate the progress of structural biology.
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Affiliation(s)
- Liang Li
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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McPherson A. The growth and preliminary investigation of protein and nucleic acid crystals for X-ray diffraction analysis. METHODS OF BIOCHEMICAL ANALYSIS 2006; 23:249-345. [PMID: 12447 DOI: 10.1002/9780470110430.ch4] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Affiliation(s)
- A Rich
- Biology Department, Massachusetts Institute of Technology, Cambridge 02139, USA
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Benight AS, Wang YS, Amaratunga M, Chattopadhyaya R, Henderson J, Hanlon S, Ikuta S. Conformation and dynamics of a left-handed Z-DNA hairpin: studies of d(CGCGCGTTTTCGCGCG) in solution. Biochemistry 1989; 28:3323-32. [PMID: 2545256 DOI: 10.1021/bi00434a030] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The physical properties of the DNA oligomer d(CGCGCGTTTTCGCGCG) in solvents containing 4 M NaClO4 and 0.1 M NaCl were investigated by proton NMR, optical melting, and circular dichroism spectroscopy. Results of these investigations are as follows: (i) The DNA hexadecamer exists as a unimolecular hairpin in either high or low salt. (ii) In high salt the stem region of the hairpin is in the left-handed Z conformation. (iii) In either high or low salt, the duplex stem of the hairpin is stabilized against melting by approximately 40 degrees C compared to the linear core duplex. The added stability of the hairpin is entropic in origin. (iv) In high salt, as the temperature is elevated, the equilibrium structure of the duplex stem of the hairpin shifts from the Z to the B conformation before melting. (v) In low salt, when the DNA duplex exists in the B conformation, attachment of a T4 single-strand loop to one end only slightly decreases (by 14%) the correlation time of the CH5-CH6 interproton vector. In high salt, when the DNA duplex exists in the Z conformation, the correlation time of the CH5-CH6 interproton vector decreases by 51%. Since these viscosity-corrected correlation times are taken to be indicators of duplex motions on the nanosecond time scale, this result directly suggests a larger amplitude of these motions is present in the duplex stem of the hairpin when it exists in the Z conformation.
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Affiliation(s)
- A S Benight
- Department of Chemistry, University of Illinois, Chicago 60680
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Abstract
The simplest form of macromolecular design involves the ligation of nucleic acids. Recent results on the concatenation of nucleic acid junctions show that these molecules can act as fairly rigid macromolecular valence clusters on the nanometer scale. These clusters can be joined to form closed stick figures in which each edge is double helical DNA or RNA and each vertex is a nucleic acid junction. The geometrical criteria for forming discrete-closed and periodic structures from these components are established. The helicity of each edge limits the possible structures that can be formed. The formation of a periodic array from nucleic acid junction building blocks is compared with the crystallization of molecular systems. This comparison leads to a new interpretation of the nature of order in the solid state for molecular crystals. The suggestion is made that the structure of a solid molecular system described by the fewest unique orthogonal (Fourier) components is the one which will be entropically favored, since it contains the least information. This is the crystalline state, with a small number of molecules per asymmetric unit. The free energy from the proposed entropic driving force responsible for this behavior is available, in principle, to correct small deviations from ideality in forming covalent crystals from nucleic acid junction components, as well as in non-bonded molecular systems. Nucleic acid junction periodic arrays provide an appropriate vehicle with which to test this interpretation.
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Affiliation(s)
- N C Seeman
- Department of Biological Sciences, State University of New York, Albany 12222
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Abstract
Crystals of alpha 1-acid glycoprotein have been grown reproducibly from delipidated protein in the presence of chlorpromazine. The crystals are large hexagonal prisms of space group either P622 or P6(2)22 and the unit cell dimensions are a = b = 101 A and C = 201 A. The unit cell is very highly hydrated and is nearly 80% solvent. It contains one molecule of protein per asymmetric unit. The crystals diffract only to low resolution, presumably reflecting the extensive hydration and accompanying disorder.
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Louie A, Ribeiro NS, Reid BR, Jurnak F. Relative affinities of all Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42947-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Dock AC, Lorber B, Moras D, Pixa G, Thierry JC, Giégé R. Crystallization of transfer ribonucleic acids. Biochimie 1984; 66:179-201. [PMID: 6204693 DOI: 10.1016/0300-9084(84)90063-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A compilation of crystallization experiments of tRNAs published in literature as well as original results are given and discussed in this paper. Up to now 17 different tRNA species originating from Escherichia coli and from the yeast Saccharomyces cerevisiae have been crystallized. All structural tRNA families are represented, namely the tRNAs with large or small extra-loops and among them the initiator tRNAs. The tRNAs with small variable loops (4 to 5 nucleotides), e.g. tRNAAsp and tRNAPhe, yield the best diffracting crystals. Crystalline polymorphism is a common feature; about 100 different crystal forms have been observed, but only 6 among them enabled structure determination studies by X-ray diffraction. Crystallization strongly depends upon experimental parameters such as the presence of polyamines and magnesium as well as upon the purity and the molecular integrity of the tRNAs. Crystals are usually obtained by vapour diffusion methods using salts (e.g. ammonium sulfate), organic solvents (e.g. isopropanol, dioxane or 2-methyl-2,4-pentane diol) or polyethylene glycol as precipitants. A methodological strategy for crystallyzing new tRNA species is described.
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Wei CH. Crystallization of two cubic forms of soybean trypsin inhibitor E-I, a member of the Bowman-Birk inhibitor family. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44675-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Holbrook SR, Kim SH. Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA. Biopolymers 1983; 22:1145-66. [PMID: 6342692 DOI: 10.1002/bip.360220410] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Wang AH, Yang CC. Crystallographic studies of snake venom proteins from Taiwan cobra (Naja nana atra). Cardiotoxin-analogue III and phospholipase A2. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)52542-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 1979; 282:680-6. [PMID: 514347 DOI: 10.1038/282680a0] [Citation(s) in RCA: 1521] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.
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Wang AH, Nathans J, van der Marel G, van Boom JH, Rich A. Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound. Nature 1978; 276:471-4. [PMID: 723928 DOI: 10.1038/276471a0] [Citation(s) in RCA: 171] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The crystal structure of a complex containing deoxy CpG and a terpyridine platinum compound (TPH) shows a DNA double helical fragment with TPH intercalated between two Watson-Crick GC base pairs. The DNA unwinding angle is 23 degrees and the pucker of the deoxyribose rings differ at the 3' and 5' ends.
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Abstract
Crystals and other regular arrangements of nucleosome cores have been obtained and analyzed in the electron microscope. Two types of regular structures have been studied in detail, the nucleosome arcs and cylinders. The latter are composed of concentric cylindrical layers of intertwined right-handed helices of nucleosome cores. These studies lead to the following conclusions and concepts. The overall structure of the nucleosome core is a short, wedge-shaped cylinder measuring about 110 by 110 by 60 angstroms. Nucleosome cores interact primarily between top and bottom planes. Nucleosome cores exhibit large conformational variability. A pivot allowing two degrees of rotational freedom is postulated in the region of the 70th base pair to account for this property of the nucleosome.
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Rosenberg JM, Dickerson RE, Greene PJ, Boyer HW. Preliminary x-ray diffraction analysis of crystalline EcoRI endonuclease. J Mol Biol 1978; 122:241-5. [PMID: 682193 DOI: 10.1016/0022-2836(78)90039-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Giege R, Moras D, Thierry JC. Yeast transfer RNAasp: a new high-resolution x-ray diffracting crystal form of a transfer RNA. J Mol Biol 1977; 115:91-6. [PMID: 336897 DOI: 10.1016/0022-2836(77)90248-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Burkey DJ, McPherson A. Crystallographic evidence for the structural isomorphism of deer and beef catalase. EXPERIENTIA 1977; 33:880-1. [PMID: 911385 DOI: 10.1007/bf01951258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Arnone A, Rogers PH, Schmidt J, Han C, Harris CM, Metzler DE. Preliminary crystallographic study of aspartate: 2-oxoglutarate aminotransferase from pig heart. J Mol Biol 1977; 112:509-13. [PMID: 875028 DOI: 10.1016/s0022-2836(77)80196-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
In this article, we have described various detailed features of the conformation of yeast tRNA(Phe) revealed by recent refinement analysis of x-ray diffraction data at 2.5 A resolution. The gross features of the molecule observed in the unrefined version have been largely confirmed and a number of new features found. The unique role of the ribose 2' hydroxyl groups in maintaining a series of nonhelical conformations in this RNA molecule has become apparent. Many of these features are a direct consequence of the geometry of the ribose phosphate backbone of RNA molecules, and these may also be found in structured regions of other RNA species as well. Special attention has been directed toward two conformational motifs revealed by this analysis. These include the striking similarity between the TpsiC and anticodon hairpin turns in the polynucleotide chain, which are stabilized by the participation of uridine in the U turn. In addition, there is frequent occurrence of an arch conformation in the polynucleotide chian which is stabilized by hydrogen bonds from 2' hydroxyl residues to phosphate groups across the base of the arch. The importance of the 2' hydroxyl interactions in defining tertiary structure is illustrated by the fact that, in the nonhelical regions, almost half of the ribose residues are involved in O2' hydrogen-bonding interactions which stabilize the conformation of the molecule.
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McPherson A, Molineux I, Rich A. Crystallization of a DNA-unwinding protein: preliminary x-ray analysis of fd bacteriophage gene 5 product. J Mol Biol 1976; 106:1077-81. [PMID: 978744 DOI: 10.1016/0022-2836(76)90354-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Quigley GJ, Wang AH, Seeman NC, Suddath FL, Rich A, Sussman JL, Kim SH. Hydrogen bonding in yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A 1975; 72:4866-70. [PMID: 1108007 PMCID: PMC388833 DOI: 10.1073/pnas.72.12.4866] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Further analysis of the three-dimensional electron density map of yeast phenylalanine tRNA is presented. Attention is focused on the several types of unique hydrogen bonding that are found in the molecule and a number of sections of the electron density map are presented. These sections are compared with an electron density map of a dinucleoside phosphate. The bases in the helical stem regions are all involved in Watson-Crick hydrogen bonding interactions with the exception of the guanine-uracil base pair. Several additional tertiary hydrogen bonding interactions are described.
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Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 1974; 185:435-40. [PMID: 4601792 DOI: 10.1126/science.185.4149.435] [Citation(s) in RCA: 644] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA 's, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNA's.
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Cramer F, Sprinzl R, Furgac N, Freist W, Saenger W, Manor PC, Sprinzl M, Sternbach H. Crystallisation of yeast phenylalanine transfer RNA. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/0005-2787(74)90122-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Quigley GJ, Suddath FL, McPherson A, Kim JJ, Sneden D, Rich A. The molecular structure of yeast phenylalanine transfer RNA in monoclinic crystals. Proc Natl Acad Sci U S A 1974; 71:2146-50. [PMID: 4525325 PMCID: PMC388404 DOI: 10.1073/pnas.71.5.2146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals. The residuals from this comparison are low enough to conclude that at 4-A resolution, the three-dimensional structure of the molecule in the monoclinic crystal is essentially the same as that in the orthorhombic crystal. In addition, a correlation coefficient calculated from intensities based on a skeletal model of the molecule also confirmed the structure in the monoclinic cell. Electron density difference maps, as well as the presence of close contacts in the anticodon loop region of the monoclinic crystal, suggest that the anticodon loop may have a slightly different conformation than that observed in the orthorhombic crystals.
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Kim SH, Quigley G, Suddath FL, McPherson A, Sneden D, Kim JJ, Weinzierl J, Rich A. Unit cell transormations in yeast phenylalanine transfer RNA crystals. J Mol Biol 1973; 75:429-32. [PMID: 4580684 DOI: 10.1016/0022-2836(73)90032-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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