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Roy P, Bhattacharyya D. Contact networks in RNA: a structural bioinformatics study with a new tool. J Comput Aided Mol Des 2022; 36:131-140. [DOI: 10.1007/s10822-021-00438-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/01/2021] [Indexed: 10/19/2022]
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2
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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Goodsell DS, Burley SK, Berman HM. Revealing structural views of biology. Biopolymers 2016; 99:817-24. [PMID: 23821527 DOI: 10.1002/bip.22338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 06/17/2013] [Indexed: 11/09/2022]
Abstract
The first protein structures were determined in the 1950s. In the decades that followed, development of new methods for sample preparation, crystallization, data collection, and structure analysis yielded tens of thousands of biomolecular structures. This short review highlights some of the major technical advances exemplified with selected structures.
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Affiliation(s)
- David S Goodsell
- RCSB Protein Data Bank and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037
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Abstract
The combination of synthetic stable branched DNA and sticky-ended cohesion has led to the development of structural DNA nanotechnology over the past 30 years. The basis of this enterprise is that it is possible to construct novel DNA-based materials by combining these features in a self-assembly protocol. Thus, simple branched molecules lead directly to the construction of polyhedrons, whose edges consist of double helical DNA and whose vertices correspond to the branch points. Stiffer branched motifs can be used to produce self-assembled two-dimensional and three-dimensional periodic lattices of DNA (crystals). DNA has also been used to make a variety of nanomechanical devices, including molecules that change their shapes and molecules that can walk along a DNA sidewalk. Devices have been incorporated into two-dimensional DNA arrangements; sequence-dependent devices are driven by increases in nucleotide pairing at each step in their machine cycles.
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Affiliation(s)
- Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, USA.
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6
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Chai D. RNA structure and modeling: progress and techniques. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:71-100. [PMID: 18929139 DOI: 10.1016/s0079-6603(08)00003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dinggeng Chai
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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7
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Morales AJ, Swairjo MA, Schimmel P. Structure-specific tRNA-binding protein from the extreme thermophile Aquifex aeolicus. EMBO J 1999; 18:3475-83. [PMID: 10369686 PMCID: PMC1171426 DOI: 10.1093/emboj/18.12.3475] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genome of the bacterium Aquifex aeolicus encodes a polypeptide which is related to a small portion of a sequence found in one prokaryotic and two eukaryotic tRNA synthetases. It also is related to a portion of Arc1p, a tRNA-binding protein believed to be important for nuclear trafficking of tRNAs. Here we cloned, expressed and purified the 111 amino acid polypeptide (designated Trbp111) and showed by ultracentrifugation analysis that it is a stable dimer in solution. The protein was also crystallized in a monoclinic lattice. X-ray diffraction analysis at 2.8 A resolution revealed a prominent non-crystallographic 2-fold axis, consistent with the presence of a symmetric homodimeric structure. Band-shift analysis with polyacrylamide gels showed that the dimer binds tRNAs, but not RNA duplexes, RNA hairpins, single-stranded RNA nor 5S rRNA. Complex formation with respect to tRNA is non-specific, with a single tRNA bound per dimer. Thus, Trbp111 is a structure-specific tRNA-binding protein. These results and other considerations raise the possibility that Trbp111 is a tRNA-specific chaperone which stabilizes the native L-shaped fold in the extreme thermophile and which has been incorporated into much larger tRNA-binding proteins of higher organisms.
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MESH Headings
- Amino Acid Sequence
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/isolation & purification
- Bacterial Proteins/metabolism
- Base Sequence
- Binding, Competitive
- Cloning, Molecular
- Crystallization
- Crystallography, X-Ray
- Dimerization
- Gram-Negative Aerobic Rods and Cocci/genetics
- Molecular Sequence Data
- Molecular Weight
- Peptides/chemistry
- Peptides/genetics
- Peptides/isolation & purification
- Peptides/metabolism
- Protein Binding
- Protein Conformation
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Substrate Specificity
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Affiliation(s)
- A J Morales
- Skaggs Institute for Chemical Biology and Departments of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA
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8
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Affiliation(s)
- A Rich
- Biology Department, Massachusetts Institute of Technology, Cambridge 02139, USA
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9
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Chapter 39 Bioinorganic chemistry: Lanthanides as probes in systems of biological interest. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/s0168-1273(79)04018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Chang CH, Beer M, Marzilli LG. Osmium-labeled polynucleotides. The reaction of osmium tetroxide with deoxyribonucleic acid and synthetic polynucleotides in the presence of tertiary nitrogen donor ligands. Biochemistry 1977; 16:33-8. [PMID: 831776 DOI: 10.1021/bi00620a006] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Osmium tetroxide in the presence of pyridine or 2,2'-bipyridine has been found to react completely with the pyrimidine moieties (thymine, uracil, and cytosine) in polynucleotides. Pyrimidine osmate ester moieties, L2OSO4-pyrimidine, were formed. The OSO4 has added across the 5,6 double bond and L=pyridine or 1/2-bipyridine. The pyridine derivatives were not stable and decomposed slowly after the OSO4-pyridine reagent was removed by gel chromatography. Labeled poly(uridylic acid) lost osmium completely during gel chromatography unless the eluent contained a high concentration of pyridine. The products formed between OSO4-bipyridine and polynucleotides were much more stable and the OS label was retained during and after gel chromatography. Both the OSO4-pyridine and OSO4-bipyridine reagents reacted more rapidly than the OSO4-CN-reagent.
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Clark BF. Correlation of biological activities with structural features of transfer RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 20:1-19. [PMID: 905565 DOI: 10.1016/s0079-6603(08)60468-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Kistenmacher TJ, Marzilli LG, Rossi M. Conformational properties of the osmium tetraoxide bispyridine ester of 1-methylthymine and a comment on the linearity of the trans O=Os=O group. BIOINORGANIC CHEMISTRY 1976; 6:347-64. [PMID: 1053544 DOI: 10.1016/s0006-3061(00)80020-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The preparation and crystal and molecular structure of the osmium tetraoxide bispyridine ester of 1-methylthymine are reported. The complex crystallizes in the triclinic system, space group P1, with a = 11.493(6)A, b = 16.655(7)A, c = 6.082(2)A, alpha = 92.07(3) degrees, beta = 90.58(3) degrees, gamma = 71.36(4) degrees, V = 1102.4 A3, Dm = 1.85(1) g cm-3, DC = 1.84 g cm-3. The unit cell contains 2 osmium tetraoxide bispyridine esters of 1-methylthymine, 2 waters of crystallization and 1 disordered pyridine of solvation. Intensities for 3814 independent reflections were collected by counter methods. The structure was solved by standard heavy-atom techniques and has been refined by full-matrix least squares, based on F, to a final R value of 0.065. The osmium complex binds as a cis osmate ester to the C(5)-C(6) bond of the methylated pyrimidine in a fashion which is expected to be similar to the binding of the complex to thymidine residues in nucleic acids. The conformation of the 1-methylthymine ester is that of a half chair with C(6) showing a substantial deviation, 0.55 A, from the best mean plane of the thymine moiety. The primary coordination sphere about the Os(VI) atom is completed by 2 axial Os=O bonds and the binding of the 2 pyridine ligands in cis positions in the equatorial plane containing the ester linkages. The O=Os=O group is substantially nonlinear, 164.0(5) degrees, and this nonlinearity is attributed to intracomplex electronic effects.
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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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Jones CR, Kearns DR. Investigation of the structure of yeast tRNAphe by nuclear magnetic resonance: paramagnetic rare earth ion probes of structure. Proc Natl Acad Sci U S A 1974; 71:4237-40. [PMID: 4610573 PMCID: PMC434366 DOI: 10.1073/pnas.71.10.4237] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The binding of paramagnetic rare earth ions to yeast tRNA(Phe) shifts some resonances in the low-field nuclear magnetic resonance spectrum that have been assigned to ring nitrogen protons of specific Watson-Crick base pairs. The changes in the nuclear magnetic resonance spectrum as the tRNA is titrated with Eu(3+) indicate that 4 (or 5) Eu(3+) ions are tightly bound, that the metal binding is in the fast exchange limit, and that the binding to different sites in the molecule is sequential rather than cooperative. The first metal bound simultaneously shifts resonances associated with the dihydrouridine and the -C-C-A stem. This permits us to conclude that the folding of the tRNA(Phe) in solution brings the phosphate backbone of the -C-C-A and the dihydrouridine stems into close proximity. A model of the three-dimensional structure of tRNA(Phe) incorporating this new information appears to be compatible with the results obtained from x-ray diffraction.
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Klug A, Robertus JD, Ladner JE, Brown RS, Finch JT. Conservation of the molecular structure of yeast phenylalanine transfer RNA in two crystal forms. Proc Natl Acad Sci U S A 1974; 71:3711-5. [PMID: 4530331 PMCID: PMC433846 DOI: 10.1073/pnas.71.9.3711] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A comparison is made between the electron density maps of the monoclinic and orthorhombic crystal forms of yeast tRNA(Phe) which have been obtained respectively by ourselves and by another group. It is concluded that the molecular structures are essentially the same in both crystals, although the models derived from the maps are not the same. The relation between the two molecular packings is discussed, and it is suggested that the intermolecular contact in the orthorhombic form which is not present in the monoclinic form, may arise through base pairing of the anticodons of neighboring molecules.
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Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 1974; 250:546-51. [PMID: 4602655 DOI: 10.1038/250546a0] [Citation(s) in RCA: 690] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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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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Suddath FL, Quigley GJ, McPherson A, Sneden D, Kim JJ, Kim SH, Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution. Nature 1974; 248:20-4. [PMID: 4594440 DOI: 10.1038/248020a0] [Citation(s) in RCA: 122] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kim SH, Quigley GJ, Suddath FL, McPherson A, Sneden D, Kim JJ, Weinzierl J, Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science 1973; 179:285-8. [PMID: 4566654 DOI: 10.1126/science.179.4070.285] [Citation(s) in RCA: 332] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
At 4 A resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 A apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a secondary structure consistent with the cloverleaf conformation; however, its folding is different from that proposed in any model. The molecule is made of two double-stranded helical regions oriented at right angles to each other in the shape of an L. One end of the L has the CCA acceptor; the anticodon loop is at the other end, and the dihydrouridine and TpsiC loops form the corner.
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