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Egli M, Zhang S. Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition. Biophys J 2022; 121:4777-4787. [PMID: 35711143 PMCID: PMC9808504 DOI: 10.1016/j.bpj.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 06/10/2022] [Indexed: 01/07/2023] Open
Abstract
Fifty years ago, the first atomic-resolution structure of a nucleic acid double helix, the mini-duplex (ApU)2, revealed details of basepair geometry, stacking, sugar conformation, and backbone torsion angles, thereby superseding earlier models based on x-ray fiber diffraction, including the original DNA double helix proposed by Watson and Crick. Just 3 years later, in 1976, Ned Seeman, John Rosenberg, and Alex Rich leapt from their structures of mini-duplexes and H-bonding motifs between bases in small-molecule structures and transfer RNA to predicting how proteins could sequence specifically recognize double helix nucleic acids. They proposed interactions between amino acid side chains and nucleobases mediated by two hydrogen bonds in the major or minor grooves. One of these, the arginine-guanine pair, emerged as the most favored amino acid-base interaction in experimental structures of protein-nucleic acid complexes determined since 1986. In this brief review we revisit the pioneering work by Seeman et al. and discuss the importance of the arginine-guanine pairing motif.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee.
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts
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2
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Berman HM, DeTitta G. Crystallographic legacy of Ned Seeman. Biophys J 2022; 121:4766-4769. [PMID: 35787471 PMCID: PMC9808496 DOI: 10.1016/j.bpj.2022.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023] Open
Abstract
We trace the career path of Nadrian Seeman, the inventor of DNA nanotechnology. The influence of his early training in crystallography and how this led to his success in creating self-assembled crystals are highlighted.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
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3
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Parkinson GN, Berman H. More than forty years of nucleic acid structural science. Bioorg Med Chem 2022; 69:116887. [PMID: 35749839 DOI: 10.1016/j.bmc.2022.116887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022]
Abstract
As scientists who have worked with Stephen Neidle over many years and stages of his career, we present our perspective of his contributions to nucleic acid structural science. We trace some of the highlights of his research on nucleic acid drug interactions and the unique insights about the importance of hydration.
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Affiliation(s)
- Gary N Parkinson
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, UK.
| | - Helen Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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4
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Developing Community Resources for Nucleic Acid Structures. Life (Basel) 2022; 12:life12040540. [PMID: 35455031 PMCID: PMC9031032 DOI: 10.3390/life12040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.
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5
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Steinert RM, Kasireddy C, Heikes ME, Mitchell-Koch KR. Newly identified C–H⋯O hydrogen bond in histidine. Phys Chem Chem Phys 2022; 24:19233-19251. [DOI: 10.1039/d2cp02048c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).
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Affiliation(s)
- Ryan M. Steinert
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Chandana Kasireddy
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Micah E. Heikes
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Katie R. Mitchell-Koch
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
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6
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Beyond the double helix: DNA structural diversity and the PDB. J Biol Chem 2021; 296:100553. [PMID: 33744292 PMCID: PMC8063756 DOI: 10.1016/j.jbc.2021.100553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/15/2021] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 68 years. Their structural diversity has extended to the demonstration of sequence-dependent local structure in duplex DNA, to DNA bending in short and long sequences and in the DNA wound round the nucleosome, and to left-handed duplex DNAs. Beyond the double helix itself, in circumstances where DNA sequences are or can be induced to unwind from being duplex, a wide variety of topologies and forms can exist. Quadruplex structures, based on four-stranded cores of stacked G-quartets, are prevalent though not randomly distributed in the human and other genomes and can play roles in transcription, translation, and replication. Yet more complex folds can result in DNAs with extended tertiary structures and enzymatic/catalytic activity. The Protein Data Bank is the depository of all these structures, and the resource where structures can be critically examined and validated, as well as compared one with another to facilitate analysis of conformational and base morphology features. This review will briefly survey the major structural classes of DNAs and illustrate their significance, together with some examples of how the use of the Protein Data Bank by for example, data mining, has illuminated DNA structural concepts.
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7
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He Y, Eloi JC, Harniman RL, Richardson RM, Whittell GR, Mathers RT, Dove AP, O’Reilly RK, Manners I. Uniform Biodegradable Fiber-Like Micelles and Block Comicelles via “Living” Crystallization-Driven Self-Assembly of Poly(l-lactide) Block Copolymers: The Importance of Reducing Unimer Self-Nucleation via Hydrogen Bond Disruption. J Am Chem Soc 2019; 141:19088-19098. [DOI: 10.1021/jacs.9b09885] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yunxiang He
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jean-Charles Eloi
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Robert L. Harniman
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Robert M. Richardson
- School of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - George R. Whittell
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Robert T. Mathers
- Department of Chemistry, The Pennsylvania State University, New Kensington, Pennsylvania 15068, United States
| | - Andrew P. Dove
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Rachel K. O’Reilly
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ian Manners
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6, Canada
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Abstract
Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.
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De Iuliis GN, Lawrance GA, Wilson NL. Metal Complex-promoted Cleavage of RNA Dimers and Trimers: Electrospray Ionisation Mass Spectrometry Evidence for Cleavage. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/1028662021000062590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Geoffry N. De Iuliis
- a Discipline of Chemistry, School of Environmental and Life Sciences , The University of Newcastle , Callaghan , 2308 , Australia
| | - Geoffrey A. Lawrance
- a Discipline of Chemistry, School of Environmental and Life Sciences , The University of Newcastle , Callaghan , 2308 , Australia
| | - Nicole L. Wilson
- a Discipline of Chemistry, School of Environmental and Life Sciences , The University of Newcastle , Callaghan , 2308 , Australia
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Altona C, Koeners HJ, de Jager JR, van Boom JH, van Binst G. Adenylyl-uridine. Assignment and analysis of the 270 Mhz fast Fourier transform proton magnetic resonance spectrum. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19740930611] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Abstract
The DNA backbone geometry was analyzed for 96 crystal structures of oligodeoxynucleotides. The ranges and mean values of the torsion angles for the observed subclasses of the A-, B-, and Z-DNA conformational types were determined by analyzing distributions of the torsion angles and scattergrams relating pairs of angles.
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Affiliation(s)
- B Schneider
- Rutgers University, Department of Chemistry, Piscataway, NJ 08855-0939, USA
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12
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Holmes RR. A square pyramidal model for ribonuclease action. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 2009; 8:445-53. [PMID: 965152 DOI: 10.1111/j.1399-3011.1976.tb02524.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A mechanism incorporating a square pyramidal model (SP) is presented for the action of bovine pancreatic ribonuclease. Its formulation is based on structural principles governing pentacoordinate behavior. The model is compared with a previous trigonal bipyramidal (TP) representation with regard to the geometry of the active site and enzyme constraints. Of two variants of the SP model, an adjacent (cis displacement) and in-line (trans displacement) process, the in-line mechanism, as with the TP model, fits existing model studies. Consideration of the energetics of the SP vs. the TP model leads to an estimated energy difference of about 1-2 kcal/mol. This suggests that the preferred model may be intermediate in geometry between the two idealized representations for the enzymatic hydrolysis. Comparisons are made showing that pseudorotation is an unlikely process in either model.
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Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (NEW YORK, N.Y.) 2008; 14:465-81. [PMID: 18192612 PMCID: PMC2248255 DOI: 10.1261/rna.657708] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 10/29/2007] [Indexed: 05/03/2023]
Abstract
A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle delta epsilon zeta alpha beta gamma delta combinations empirically found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for delta epsilon zeta and a lowercase letter for alpha beta gamma delta, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.
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Affiliation(s)
- Jane S Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710-3711, USA.
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Anbarasu A, Anand S, Rao S. Investigations on unconventional hydrogen bonds in RNA binding proteins: The role of CH⋯OC interactions. Biosystems 2007; 90:792-801. [PMID: 17555865 DOI: 10.1016/j.biosystems.2007.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 04/16/2007] [Accepted: 04/18/2007] [Indexed: 11/16/2022]
Abstract
We have investigated the roles played by C-H...O=C interactions in RNA binding proteins. There was an average of 78 CH...O=C interactions per protein and also there was an average of one significant CH...O=C interactions for every 6 residues in the 59 RNA binding proteins studied. Main chain-Main chain (MM) CH...O=C interactions are the predominant type of interactions in RNA binding proteins. The donor atom contribution to CH...O=C interactions was mainly from aliphatic residues. The acceptor atom contribution for MM CH...O=C interactions was mainly from Val, Phe, Leu, Ile, Arg and Ala. The secondary structure preference analysis of CH...O=C interacting residues showed that, Arg, Gln, Glu and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Ile, Leu, Lys, Met, Phe, Trp and Val preferred to be in strand conformation. Most of the CH...O=C interacting polar amino acid residues were solvent exposed while, majority of the CH...O=C interacting non polar residues were excluded from the solvent. Long and medium-range CH...O=C interactions are the predominant type of interactions in RNA binding proteins. More than 50% of CH...O=C interacting residues had a higher conservation score. Significant percentage of CH...O=C interacting residues had one or more stabilization centers. Sixty-six percent of the theoretically predicted stabilizing residues were also involved in CH...O=C interactions and hence these residues may also contribute additional stability to RNA binding proteins.
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Affiliation(s)
- Anand Anbarasu
- School of Bio-Technology, Chemical and Bio-Medical Engineering, VIT University, Vellore 632014, India
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15
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Sychrovský V, Vokácová Z, Sponer J, Spacková N, Schneider B. Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids. J Phys Chem B 2007; 110:22894-902. [PMID: 17092041 DOI: 10.1021/jp065000l] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Kim SH. Three-dimensional structure of transfer RNA and its functional implications. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 46:279-315. [PMID: 205095 DOI: 10.1002/9780470122914.ch4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Goswami S, Ghosh K, Mukherjee R. Novel Motif of Hydrogen Bonds in the Water-assisted Supramolecular Self-assembly of 2-acetylamino-6-methylpyridine-N-oxide and Hetero-assembly of 1:1 Co-crystal of o-Phenylenediamine with Catechol. Supramol Chem 2006. [DOI: 10.1080/10610270008049129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Shyamaprosad Goswami
- a Department of Chemistry , Bengal Engineering College (Deemed University) , Howrah, 711103, India
| | - Kumaresh Ghosh
- a Department of Chemistry , Bengal Engineering College (Deemed University) , Howrah, 711103, India
| | - Reshmi Mukherjee
- a Department of Chemistry , Bengal Engineering College (Deemed University) , Howrah, 711103, India
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18
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Affiliation(s)
- Thomas Steiner
- a Institut für Kristallographie, Freie Universität Berlin , Takustraβe 6, D-14195 , Berlin , Germany
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19
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Giraldo J, De Maria L, Wodak SJ. Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase. Proteins 2004; 56:261-76. [PMID: 15211510 DOI: 10.1002/prot.20137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The microbial ribonuclease barnase exhibits low catalytic activity toward GpN dinucleotides, where G is guanosine, p is phosphate and N represents any nucleoside. When a phosphate is added to the 3'-end, as in GpNp, substrate affinity is enhanced by one order of magnitude, and the catalytic rate by two. In order to gain insight into this phenomenon, we analyzed the nucleotide conformations and protein-nucleotide interactions of 4 ns molecular dynamics (MD) trajectories of complexes of barnase with guanylyl(3'-5') adenosine (GpA) and guanylyl(3'-5') adenosine 3'-monophosphate (GpAp), respectively, in the presence of solvent and counter ions. We found that, in a majority of the bound GpA conformations, the guanine base was firmly bound to the recognition site. The phosphate and adenosine moieties pointed into the solvent, and interactions with key catalytic residues were absent. In contrast, the bound GpAp adopted conformations in which all of the nucleotide portions remained tightly bound to the enzyme and interactions with key catalytic residues were maintained. These observations indicate that, for GpA, a significant proportion of the bound nucleotide adopts non-productive conformations and that adding the terminal phosphate as in GpAp shifts the equilibrium of the bound conformations towards structures capable of undergoing catalysis. Incorporating this property into the kinetic equations yields an increase in both the apparent rate constant (kcat) and the apparent dissociation constant (K(M)) for GpAp versus GpA. The increase in K(M), caused by the presence of additional non-productive binding modes for GpA, should however be counterbalanced by the propensity of free GpA to adopt folded conformations in solution, which are unable to bind the enzyme and by the tighter binding of GpAp (Giraldo J, Wodak SJ, Van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998; 283:863-882). Addition of the terminal phosphate is shown to significantly influence the collective motion of the enzyme in a manner that fosters interactions with key catalytic residues, representing a further likely contribution to the catalytic rate enhancement.
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Affiliation(s)
- Jesús Giraldo
- Grup de Modelització Estructural i Funcional de Sistemes Biològics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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20
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Ge W, Schneider B, Olson WK. Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. Biophys J 2004; 88:1166-90. [PMID: 15501936 PMCID: PMC1305121 DOI: 10.1529/biophysj.104.043612] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Elastic ellipsoidal functions defined by the observed hydration patterns around the DNA bases provide a new basis for measuring the recognition of ligands in the grooves of double-helical structures. Here a set of knowledge-based potentials suitable for quantitative description of such behavior is extracted from the observed positions of water molecules and amino acid atoms that form hydrogen bonds with the nitrogenous bases in high resolution crystal structures. Energies based on the displacement of hydrogen-bonding sites on drugs in DNA-crystal complexes relative to the preferred locations of water binding around the heterocyclic bases are low, pointing to the reliability of the potentials and the apparent displacement of water molecules by drug atoms in these structures. The validity of the energy functions has been further examined in a series of sequence substitution studies based on the structures of DNA bound to polyamides that have been designed to recognize the minor-groove edges of Watson-Crick basepairs. The higher energies of binding to incorrect sequences superimposed (without conformational adjustment or displacement of polyamide ligands) on observed high resolution structures confirm the hypothesis that the drug subunits associate with specific DNA bases. The knowledge-based functions also account satisfactorily for the measured free energies of DNA-polyamide association in solution and the observed sites of polyamide binding on nucleosomal DNA. The computations are generally consistent with mechanisms by which minor-groove binding ligands are thought to recognize DNA basepairs. The calculations suggest that the asymmetric distributions of hydrogen-bond-forming atoms on the minor-groove edge of the basepairs may underlie ligand discrimination of G.C from C.G pairs, in addition to the commonly believed role of steric hindrance. The analysis of polyamide-bound nucleosomal structures reveals other discrepancies in the expected chemical design, including unexpected contacts to DNA and modified basepair targets of some ligands. The ellipsoidal potentials thus appear promising as a mathematical tool for the study of drug- and protein-DNA interactions and for gaining new insights into DNA-binding mechanisms.
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Affiliation(s)
- Wei Ge
- Department of Chemistry & Chemical Biology, Rutgers, the State University of New Jersey, Wright-Rieman Laboratories, Piscataway, New Jersey, USA
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21
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Freisinger E, Grollman AP, Miller H, Kisker C. Lesion (in)tolerance reveals insights into DNA replication fidelity. EMBO J 2004; 23:1494-505. [PMID: 15057282 PMCID: PMC391067 DOI: 10.1038/sj.emboj.7600158] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Accepted: 02/12/2004] [Indexed: 01/07/2023] Open
Abstract
The initial encounter of an unrepaired DNA lesion is likely to be with a replicative DNA polymerase, and the outcome of this event determines whether an error-prone or error-free damage avoidance pathway is taken. To understand the atomic details of this critical encounter, we have determined the crystal structures of the pol alpha family RB69 DNA polymerase with DNA containing the two most prevalent, spontaneously generated premutagenic lesions, an abasic site and 2'-deoxy-7,8-dihydro-8-oxoguanosine (8-oxodG). Identification of the interactions between these damaged nucleotides and the active site provides insight into the capacity of the polymerase to incorporate a base opposite the lesion. A novel open, catalytically inactive conformation of the DNA polymerase has been identified in the complex with a primed abasic site template. This structure provides the first molecular characterization of the DNA synthesis barrier caused by an abasic site and suggests a general mechanism for polymerase fidelity. In contrast, the structure of the ternary 8-oxodG:dCTP complex is almost identical to the replicating complex containing unmodified DNA, explaining the relative ease and fidelity by which this lesion is bypassed.
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Affiliation(s)
- Eva Freisinger
- Department of Pharmacological Sciences, Center for Structural Biology, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Arthur P Grollman
- Laboratory of Chemical Biology, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Holly Miller
- Laboratory of Chemical Biology, SUNY at Stony Brook, Stony Brook, NY, USA
- Laboratory of Chemical Biology, Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA. Tel.: +1 631 444 6665; Fax: +1 631 444 4671; E-mail:
| | - Caroline Kisker
- Department of Pharmacological Sciences, Center for Structural Biology, SUNY at Stony Brook, Stony Brook, NY, USA
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA. Tel.:+1 631 632 1465; Fax: +1 631 632 1555; E-mail:
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Abstract
RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available.
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Affiliation(s)
- Bohdan Schneider
- Center for Complex Molecular Systems and Biomolecules and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n.2, CZ-16610 Prague, Czech Republic.
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24
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Shi Z, Olson CA, Bell AJ, Kallenbach NR. Non-classical helix-stabilizing interactions: C-H...O H-bonding between Phe and Glu side chains in alpha-helical peptides. Biophys Chem 2002; 101-102:267-79. [PMID: 12488007 DOI: 10.1016/s0301-4622(02)00171-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The classical picture of H-bonds has evolved considerably. In contrast to earlier expectations, C-H...O H-bonds are now known to be prevalent in both small organic and large biological systems. However, there are few reports on the energetic contribution of C-H...O H-bonds in protein or polypeptide systems and we do not know whether such interactions are stabilizing. Here we investigate C-H...O H-bonding interactions between Phe and Glu side chains by determining their effects on the helicity of model alpha-helical peptides using a combination of CD and NMR spectroscopy. The results suggest that Glu/Phe C-H...O H-bonding interactions stabilize helical structure, but only in the orientation Glu --> Phe (N --> C). Each Glu --> Phe (N --> C) interaction can contribute approximately -0.5 kcal mol(-1) to the stability of helical peptide. In the reverse orientation, Phe --> Glu (N --> C) appears to contribute negligibly. pH titrations provide further evidence for the existence of C-H...O H-bonds. The C-H...O H-bonding interactions in these peptides are insensitive to the screening effect of added neutral salt. Our results provide quantitative energetic information on C-H...O H-bonds that should be useful for empirical force-field calibration.
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, New York, NY 10003, USA
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25
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Dvir H, Wong DM, Harel M, Barril X, Orozco M, Luque FJ, Muñoz-Torrero D, Camps P, Rosenberry TL, Silman I, Sussman JL. 3D structure of Torpedo californica acetylcholinesterase complexed with huprine X at 2.1 A resolution: kinetic and molecular dynamic correlates. Biochemistry 2002; 41:2970-81. [PMID: 11863435 DOI: 10.1021/bi011652i] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Huprine X is a novel acetylcholinesterase (AChE) inhibitor, with one of the highest affinities reported for a reversible inhibitor. It is a synthetic hybrid that contains the 4-aminoquinoline substructure of one anti-Alzheimer drug, tacrine, and a carbobicyclic moiety resembling that of another AChE inhibitor, (-)-huperzine A. Cocrystallization of huprine X with Torpedo californica AChE yielded crystals whose 3D structure was determined to 2.1 A resolution. The inhibitor binds to the anionic site and also hinders access to the esteratic site. Its aromatic portion occupies the same binding site as tacrine, stacking between the aromatic rings of Trp84 and Phe330, whereas the carbobicyclic unit occupies the same binding pocket as (-)-huperzine A. Its chlorine substituent was found to lie in a hydrophobic pocket interacting with rings of the aromatic residues Trp432 and Phe330 and with the methyl groups of Met436 and Ile439. Steady-state inhibition data show that huprine X binds to human AChE and Torpedo AChE 28- and 54-fold, respectively, more tightly than tacrine. This difference stems from the fact that the aminoquinoline moiety of huprine X makes interactions similar to those made by tacrine, but additional bonds to the enzyme are made by the huperzine-like substructure and the chlorine atom. Furthermore, both tacrine and huprine X bind more tightly to Torpedo than to human AChE, suggesting that their quinoline substructures interact better with Phe330 than with Tyr337, the corresponding residue in the human AChE structure. Both (-)-huperzine A and huprine X display slow binding properties, but only binding of the former causes a peptide flip of Gly117.
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Affiliation(s)
- H Dvir
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
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26
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Foloppe N, Hartmann B, Nilsson L, MacKerell AD. Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J 2002; 82:1554-69. [PMID: 11867468 PMCID: PMC1301954 DOI: 10.1016/s0006-3495(02)75507-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The glycosyl torsion (chi) in nucleic acids has long been recognized to be a major determinant of their conformational properties. chi torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with gamma in the g(+) and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When gamma is changed from g(+) to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10 kcal/mol and tends to be lower with purines than with pyrimidines. With gamma = g(+)/chi = anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between chi values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that gamma = trans/chi = anti is a minor but not negligible conformation. Overall, chi appears to be a very malleable structural parameter with the experimental chi distributions reflecting, to a large extent, the associated intrinsic torsional energetics.
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Affiliation(s)
- Nicolas Foloppe
- Center for Structural Biology, Department of Bioscience, Karolinska Institutet, S-141 57, Huddinge, Sweden
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27
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Abstract
Although the peptide C(alpha)H group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH..O interaction. The preferred H-bond lengths are quite uniform, about 3.32 A. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the C(alpha)H stretching frequency, potential diagnostics of the presence of such an H-bond within a protein.
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Affiliation(s)
- S Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300, USA.
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28
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Abstract
The current state of three-dimensional structure analysis of RNA by x-ray crystallography is summarized. The methods of sample preparation, crystallization, data collection, and structure solution are discussed, followed by a review of the RNA structures that have been determined and of common structural features, and finally, an appraisal of future prospects for x-ray crystal structure analysis of RNA.
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Affiliation(s)
- S R Holbrook
- Structural Biology Division, Lawrence Berkeley National Laboratory, University of California at Berkeley 94720, USA
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29
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Krishnan R, Seshadri T. A parallel stranded 2′-5′ double helical model for poly A: crystal structure of adenylyl-2′,5′-adenosine trihydrate and comparison with the tetrahydrate structure. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(99)00357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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30
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Müller A, Talbot F, Leutwyler S. Intermolecular vibrations of jet-cooled (2-pyridone)2: A model for the uracil dimer. J Chem Phys 2000. [DOI: 10.1063/1.480524] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Foloppe N, MacKerell AD. Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics. J Phys Chem B 1999. [DOI: 10.1021/jp992716q] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicolas Foloppe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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32
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Garland CS, Tarien E, Nirmala R, Clark P, Rifkind J, Eichhorn GL. Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase. Biochemistry 1999; 38:3421-5. [PMID: 10079088 DOI: 10.1021/bi9820098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A frequently used schematic model of transcriptional elongation shows an RNA polymerase molecule moving along a linear DNA. This model is of course highly idealized and not compatible with promoter sequences [Gralla, J. D. (1991) Cell 66, 415-418; Schleif, R. (1992) Annu. Rev. Biochem. 61, 199-223] and regulatory proteins [Koleske, A. J., and Young, R. A. (1995) Trends Biochem. Sci. 20, 113-116; Dunaway, M., and Dröge, P. (1989) Nature 341, 657-659; Müller, H. P., Sogo, J. M., and Schaffner, W. (1989) Cell 58, 767-777] located some distance away from the point of transcription initiation [Karsten, R., von Hippel, P. H., and Langowski, J. (1995) Trends Biochem. Sci. 20, 500-506]. These circumstances lead to the expectation of curvature along the DNA strand and require looping between sometimes distant points. We have now shown curvature in a dinucleotide formed at the very onset of transcription when it is poised for reaction with a mononucleotide to form a trinucleotide. The curvature became evident from the demonstration that a metal ion bound with a mononucleotide in the i+1 (elongation) site is approximately equidistant from bases at the 5' end (i-1 site) and 3' end (i site) of the dinucleotide. Similar results were obtained with three different dinucleotides and four mononucleotides. Curvature of the RNA initiate may reflect curvature of the DNA to which it is bound. These studies show curvature to be a significant feature in the interaction between DNA template and RNA elongate even at the very beginning of transcription.
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Affiliation(s)
- C S Garland
- Laboratory of Cellular and Molecular Biology, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland 21224, USA
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33
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Giraldo J, Wodak SJ, van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998; 283:863-82. [PMID: 9790845 DOI: 10.1006/jmbi.1998.2139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-stranded RNA. Its very low catalytic activity toward GpN dinucleotides, where N stands for any nucleoside, is markedly increased when a phosphate is added to the 3'-end, as in GpNp. Here we investigate the conformational properties of GpA and GpAp in solution, in order to determine whether differences in these properties may be related to the changes in enzymatic activity. Two independent 1.3 ns molecular dynamics trajectories are generated for each dinucleotide in the presence of explicit water molecules and counter ions. These trajectories are analysed by monitoring molecular properties, such as the solvent accessible surface area, the distance and orientation between the bases, the behaviour of torsion angles and formation of intramolecular H-bonds. To identify relevant correlations between these parameters, statistical techniques, comprising multiple regression, clustering and discriminant analysis are used. Results show that GpA has a significant propensity to form folded conformations (approximately 50%), fostered by a small number of intramolecular H-bonds, whereas GpAp remains essentially extended. The latter behaviour seems to be due to an H-bond between the terminal phosphate and adenosine ribose group, which restricts rotation about the adenine Agamma angle. We also find that GpA folding is induced by a concerted motion of specific torsion angles, which is closely coupled to the formation of a network of flexible hydrogen bonds. Finally, on the basis of an expression for barnase KM, which incorporates the folded/extended conformational equilibria of the dinucleotide substrates, it is argued that our findings on the differences between these equilibria, can qualitatively rationalize the experimentally measured differences in enzymatic properties.
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Affiliation(s)
- J Giraldo
- Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles CP160/16, Avenue F. D. Roosevelt, 50, Bruxelles, B-1050, Belgium
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34
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Liu DX, Jiang H, Wang QM, Chen KX, Ji RY. Interpreting the effect of methyl group at the three carbon bridge of (-)-huperzine A on its anticholinesterase activity by molecular dynamics method. Bioorg Med Chem Lett 1998; 8:419-22. [PMID: 9871590 DOI: 10.1016/s0960-894x(98)00042-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Based on the recently resolved crystal structure of complex (-)-huperzine A-AChE, we simulated the interaction between (-)-huperzine A analogues and AChE using molecular dynamics method. It was revealed that the methyl group at the three carbon bridge of (-)-huperzine A can form a weak hydrogen bond with the phenol hydroxyl oxygen of Tyr121 and the main-chain oxygen of Gly118 of AChE, respectively.
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Affiliation(s)
- D X Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
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35
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Ushizawa K, Ueda T, Tsuboi M. Polarized Raman spectrum of single crystal uridylyl (3′–5′) adenosine: Local Raman tensors of some functional groups. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199802)45:2<135::aid-bip4>3.0.co;2-t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Raves ML, Harel M, Pang YP, Silman I, Kozikowski AP, Sussman JL. Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A. NATURE STRUCTURAL BIOLOGY 1997; 4:57-63. [PMID: 8989325 DOI: 10.1038/nsb0197-57] [Citation(s) in RCA: 257] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
(-)-Huperzine A (HupA) is found in an extract from a club moss that has been used for centuries in Chinese folk medicine. Its action has been attributed to its ability to strongly inhibit acetylcholinesterase (AChE). The crystal structure of the complex of AChE with optically pure HupA at 2.5 A resolution shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. This structure is compared to the native structure of AChE devoid of any inhibitor as determined to the same resolution. An analysis of the affinities of structural analogues of HupA, correlated with their interactions with the protein, shows the importance of individual hydrophobic interactions between HupA and aromatic residues in the active-site gorge of AChE.
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Affiliation(s)
- M L Raves
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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37
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Chou SH, Zhu L, Gao Z, Cheng JW, Reid BR. Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. J Mol Biol 1996; 264:981-1001. [PMID: 9000625 DOI: 10.1006/jmbi.1996.0691] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The DNA undecamers GTACAAAGTAC (AAA 11-mer) and GTACGAGGTAC (GAG 11-mer) have been studied in solution by high-resolution NMR spectroscopy. Both duplexes form stable hairpins containing single deoxyadenosine loops and stems containing five base-pairs that are closed at the loop end by sheared AxA and GxC pairs, respectively. These molecules thus contain new AAA and GAG loop turn motifs. All protons, including the chiral H5'/H5" protons of the loop residues, were assigned using NOESY, DQF-COSY and heteronuclear 1H-31P COSY experiments. The backbone torsion angles were constrained using experimental data from NOE crosspeaks, three-bond 1H-1H coupling constants and four-bond 1H-31P coupling constants and four-bond 1H-31P coupling constants. The AAA and GAG 11-mers form similar structures in solution. The detailed structure of the AAA 11-mer was determined by the combined use of NMR, distance geometry and energy minimization methods. This structure exhibits good stacking of the loop adenosine base on the closing 5Ax7A sheared pair, with the 6A base stacking on the 5A base and the 6A deoxyribose stacking with the 7A base. All sugars in the AAA 11-mer hairpin adopt the typical DNA C2'-endo conformation and a sharp backbone turn occurs between residues 6A and 7A. This loop turn is brought about mainly by a change in the backbone phosphate torsion angles from zeta(g-) alpha(g-) to zeta(g+) alphat(g+) at the turn. The gamma torsion angle of residue 7A in the closing sheared pair also changes from gauche+ to trans. In Pu1NPu2 loop turns of the GCA, AAA and GAG types, the chemical shift of the H4' proton of the loop deoxyribose depends on the nature of Pu2; this reflects the stacking of the loop sugar on the Pu2 base and the different ring current effects of A or G in this position.
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Affiliation(s)
- S H Chou
- Biochemistry Department, University of Washington, Seattle 98195, USA
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38
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Zhu L, Chou SH, Reid BR. A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins. Proc Natl Acad Sci U S A 1996; 93:12159-64. [PMID: 8901550 PMCID: PMC37960 DOI: 10.1073/pnas.93.22.12159] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Recently, we established that satellite III (TGGAA)n tandem repeats, which occur at the centromeres of human chromosomes, pair with themselves to form an unusual "self-complementary" antiparallel duplex containing (GGA)2 motifs in which two unpaired guanines from opposite strands intercalate between sheared G.A base pairs. In separate studies, we have also established that the GCA triplet does not form bimolecular (GCA)2 motifs but instead promotes the formation of hairpins containing a GCA-turn motif in which the loop contains a single cytidine closed by a sheared G.A pair. Since TGCAA is the most frequent variant of TGGAA found in satellite III repeats, we reasoned that the potential of this variant to form GCA-turn miniloop fold-back structures might be an important factor in modulating the local structure in natural (TGGAA)n repeats. We report here the NMR-derived solution structure of the heptadecadeoxynucleotide (G)TGGAATGCAATGGAA(C) in which a central TGCAA pentamer is flanked by two TGGAA pentamers. This 17-mer forms a rather unusual and very stable hairpin structure containing eight base pairs in the stem, only four of which are Watson-Crick pairs, and a loop consisting of a single cytidine residue. The stem contains a (GGA)2 motif with intercalative 14G/4G stacking between two sheared G.A base pairs; the loop end of the stem consists of a sheared 8G.10A closing pair with the cytosine base of the 9C loop stacked on 8G. The remarkable stability of this unusual hairpin structure (Tm = 63 degrees C) suggests that it probably plays an important role in modulating the folding of satellite III (TGGAA)n repeats at the centromere.
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Affiliation(s)
- L Zhu
- Chemistry Department, University of Washington, Seattle 98195, USA
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39
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Leonard † NJ, Neelima. Methodology for the Synthesis of Dinucleoside Monophosphates Containing A 2′-Deoxy-3-Isoadenosine Unit: 3-iso-dApT and Tp(3-iso-dA). ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Holmes RR, Deiters JA, Gallucci JC. COMPUTER SIMULATION OF RIBONUCLEASE ACTION ON URIDYLYL-(3′-5′)-ADENOSINE. PHOSPHORUS SULFUR 1995. [DOI: 10.1080/10426509508036948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Robert R. Holmes
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
| | - Joan A. Deiters
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
| | - Judith C. Gallucci
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
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41
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Steiner T, Starikov EB, Amado AM, Teixeira-Dias JJC. Weak hydrogen bonding. Part 2. The hydrogen bonding nature of short C–H ⋯π contacts: crystallographic, spectroscopic and quantum mechanical studies of some terminal alkynes. ACTA ACUST UNITED AC 1995. [DOI: 10.1039/p29950001321] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Krishnan R, Seshadri TP. Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase. J Biomol Struct Dyn 1993; 10:727-45. [PMID: 8466676 DOI: 10.1080/07391102.1993.10508003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.
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Affiliation(s)
- R Krishnan
- Department of Physics, Indian Institute of Science, Bangalore
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43
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Erie DA, Breslauer KJ, Olson WK. A Monte Carlo method for generating structures of short single-stranded DNA sequences. Biopolymers 1993; 33:75-105. [PMID: 8427940 DOI: 10.1002/bip.360330109] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by +/- 10 degrees in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (3(7)) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5' end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 10(6) conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques.
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Affiliation(s)
- D A Erie
- Department of Chemistry, Rutgers, State University of New Jersey, New Brunswick 08903
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44
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Abstract
The chemical stability of phosphodiester bonds of some oligoribonucleotides in the presence of a cofactor like polyvinylpyrolidine (PVP) is sequence dependent. It was found that pyrimidine-A (YA) and pyrimidine-C (YC) are especially susceptible to hydrolysis. The hydrolyzability of this same phosphodiester bond is dependent on its position in the oligomer. The presence of 3' and 5'-adjacent nucleotides enhances hydrolysis of the UA phosphodiester bond. The acceleration of the hydrolysis of UA by a 5'-adjacent nucleotide is not base dependent. However, a 3'-adjacent purine increases hydrolysis of a UA phosphodiester bond more than a 3'-pyrimidine. The presence of the exoamino group on the 3'-side base (on 6 and 4 position for adenosine and cytidine, respectively) of YA or YZ phosphodiester bond is required for hydrolysis.
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Affiliation(s)
- R Kierzek
- Department of Chemistry, University of Rochester, NY 14627-0216
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45
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Abstract
Selective cleavage of phosphodiester bonds in RNA is important in the processing of large RNA molecules. This paper reports specific cleavage at UA sequences in single stranded oligoribonucleotides as short as hexamers. The hydrolysis between U and A leaves a 2',3'-cyclic phosphate on the 5'-side and a 5'-hydroxyl group on the 3' side of the cleavage. The hydrolysis is promoted by a wide range of cofactors, including polymeric organic compounds such as polyvinylpyrrolydone (PVP) and by proteins. A variety of experiments suggests the cleavage is not due to contamination by ribonuclease. The rate of cleavage is a function of oligoribonucleotide, PVP and spermidine concentrations. Mg2+ is not required. The phenomenon described here can potentially provide a relatively simple way of coding chemical stability into single stranded RNA based on its sequence and structure. This process seems to be similar to that involved in post-transcriptional degradation of mRNA.
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Affiliation(s)
- R Kierzek
- Department of Chemistry, University of Rochester, NY 14627-0216
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46
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Berman HM, Sussman JL, Joshua-Tor L, Revich GG, Ripley LS. A structural model for sequence-specific proflavin-DNA interactions during in vitro frameshift mutagenesis. J Biomol Struct Dyn 1992; 10:317-31. [PMID: 1466812 DOI: 10.1080/07391102.1992.10508650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Molecular models describing intermediates that may lead to proflavin-induced 1 bp deletions during in vitro polymerization by E. coli DNA polymerase I Klenow fragment are proposed. The models provide structural explanations for the fact that the induced frameshifts always occur opposite template bases that are adjacent to 5' pyrimidines and are based on the underlying hypothesis that the deletions arise because the polymerase passes by a template base without copying it. Because the most frequent mutations are opposite Pu in the template sequence 5' Py Pu 3', a single-strand loop-out model was constructed for this sequence and proflavin was added, using structures found in crystalline oligonucleotides and their complexes with proflavin. The model seeks to rationalize the roles of the 5' pyrimidine and proflavin in facilitating the bypass. Four potential roles for proflavin in mutagenesis are described: 1) stacking on the looped-out base; 2) stacking on the base pair immediately preceding the site of mutation; 3) hydrogen bonding with the 5' pyrimidine; 4) hydrogen bonding with the phosphate backbone. These models point to the possibility that a number of proflavin-DNA interactions may be involved. In contrast, modeling does not suggest a role for classically intercalated proflavin in frameshift mutagenesis arising during in vitro DNA polymerization.
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Affiliation(s)
- H M Berman
- Department of Chemistry, Rutgers University, Piscataway, NJ 08855-0939
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47
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Joshua-Tor L, Frolow F, Appella E, Hope H, Rabinovich D, Sussman JL. Three-dimensional structures of bulge-containing DNA fragments. J Mol Biol 1992; 225:397-431. [PMID: 1593627 DOI: 10.1016/0022-2836(92)90929-e] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The three-dimensional structure of a DNA tridecamer d(CGCAGAATTCGCG)2 containing bulged adenine bases was determined by single crystal X-ray diffraction methods, at 120 K, to 2.6 A resolution. The structure is a B-DNA type double helix with a single duplex in the asymmetric unit. One of the bulged adenine bases loops out from the double helix, while the other stacks in to it. This is in contrast to our preliminary finding, which indicated that both adenine bases were looped out. This revised model was confirmed by the use of a covalently bound heavy-atom derivative. The conformation of the looped-out bulge hardly disrupts base stacking interactions of the bases flanking it. This is achieved by the backbone making a "loop-the-loop" curve with the extra adenine flipping over with respect to the other nucleotides in the strand. The looped-out base intercalates into the stacked-in bulge site of a symmetrically related duplex. The looped-out and stacked-in bases form an A.A reversed Hoogsteen base-pair that stacks between the surrounding base-pairs, thus stabilizing both bulges. The double helix is frayed at one end with the two "melted" bases participating in intermolecular interactions. A related structure, of the same tridecamer, after soaking the crystals with proflavin, was determined to 3.2 A resolution. The main features of this B-DNA duplex are basically similar to the native tridecamer but differ in detail especially in the conformation of the bulged-out base. Accommodation of a large perturbation such as that described here with minimal disruption of the double helix shows both the flexibility and resiliency of the DNA molecule.
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Affiliation(s)
- L Joshua-Tor
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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48
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Kawai G, Hashizume T, Yasuda M, Miyazawa T, McCloskey JA, Yokoyama S. Conformational Rigidity of N4-Acetyl-2′-O-methylcytidine Found in tRNA of Extremely Thermophilic Archaebacteria (Archaea). ACTA ACUST UNITED AC 1992. [DOI: 10.1080/07328319208021740] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Blommers MJ, van de Ven FJ, van der Marel GA, van Boom JH, Hilbers CW. The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT). EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 201:33-51. [PMID: 1915376 DOI: 10.1111/j.1432-1033.1991.tb16253.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The hairpin formed by d(ATCCTATTTATAGGAT) was studied by means of two-dimensional NMR spectroscopy and conformational analysis. Almost all 1H resonances of the stem region could be assigned, while the 1H and 31P spectra of the loop region were interpreted completely; this includes the stereospecific assignment of the H5' and H5" resonances. The derivation of the detailed loop structure was carried out in a stepwise fashion including some improved and new methods for structure determination from NMR data. In the first step, the mononucleotide structures were examined. The conformational space available to the mononucleotide was scanned systematically by varying the glycosidic torsion angle and pseudorotational parameters. Each generated conformer was tested against the experimental J coupling constants and NOE parameters. In the following stage, the structures of dinucleotides and longer fragments were derived. Inter-residue distances between protons were calculated by means of a procedure in which the simulated NOEs, obtained via a relaxation-matrix approach, were fitted to the experimental NOEs without the introduction of a molecular model. In addition, the backbone torsion angles beta, gamma and epsilon were deduced from homocoupling and heterocoupling constants. These data served as constraints in the next step, in which the loop sequence was subjected to a multi-conformer generation procedure. The resulting structures were tested against the mentioned constraints and disregarded if these constraints were violated. This yielded a family of structures for the loop region, confined to a relatively narrow conformational space. A representative conformation was subsequently docked on a B-type stem which fulfilled the structural constraints (derived from the NMR experiments for the stem region) to yield the hairpin structure. Results obtained from subsequent restrained-molecular-mechanics as well as free-molecular-mechanics calculations are in accordance with those obtained by means of the analysis described above. The structure of the hairpin loop is a compactly folded conformation and the first base of the central TTTA region forms a Hoogsteen T-A pair with the fourth base. This Hoogsteen base pair is stacked upon the sixth base pair of the B-type double-helical stem. The second base of the loop is folded into the minor groove, whereas the third base of the loop is partly stacked on the first and fourth bases. The phosphate backbone exhibits a sharp turn between the third and fourth nucleotides of the loop. The peculiar structure of this hairpin loop is discussed in relation to loop folding in DNA and RNA hairpins and in relation to a general model for loop folding.
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Affiliation(s)
- M J Blommers
- N.S.R. Center for Molecular Design, Structure and Synthesis, University of Nijmegen, The Netherlands
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50
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Nucleoside and nucleotide transport through a model liquid membrane. Periodic-catastrophic transport of a novel amantadine phosphoramidate conjugate of 5'-AMP. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1061:95-105. [PMID: 1995060 DOI: 10.1016/0005-2736(91)90273-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Adenosine 5'-phosphor(adamantyl)amidate (5), an analog derived by linking the antiviral drug amantadine to 5'-AMP is transported through a model membrane system in a discontinuous periodic-catastrophic fashion. The system was composed of a glass cell containing two aqueous buffer phases separated by a chloroform layer. A more lipophilic, but structurally related derivative, adenosine 5'-phosphor(n-decyl)amidate (3) showed linear transport in the same system. Less lipophilic substances, including 5'-AMP and adenosine 5'-phosphor(morpholidyl)amidate (2), did not show transport. It is hypothesized that the periodic-catastrophic transport is a result of the collective activity of amidate 5 at the interface between the first aqueous interface and the chloroform layer. The time between catastrophic events is thought to be a reflection of the time necessary for molecular organization at the interface. The phenomenon is a new example of molecular organization in a system far from equilibrium leading to a repetitive dynamic process.
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