Related ArticlesThree-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics.
Protein Sci. 1996 Aug;5(8):1633-47
Authors: Toiron C, González C, Bruix M, Rico M
The three-dimensional structure of the complexes of ribonuclease A with cytidyl-2',5'-adenosine (2',5'-CpA) and deoxycytidyl-3',5'-deoxyadenosine [3',5'-d(CpA)] in aqueous solution has been determined by 1H NMR methods in combination with restrained molecular dynamics calculations. Twenty-three intermolecular NOE cross-corrections for the 3',5'-d(CpA) complex and 19 for the 2',5'-CpA, together with about 1,000 intramolecular NOEs assigned for each complex, were translated into distance constraints and used in the calculation. No significant changes in the global structure of the enzyme occur upon complex formation. The side chains of His 12, Thr 45, His 119, and the amide backbone group of Phe 120 are involved directly in the binding of the ligands at the active site. The conformation of the two bases is anti in the two complexes, but differs from the crystal structure in the conformation of the two sugar rings in 3',5'-d(CpA), shown to be in the S-type region, as deduced from an analysis of couplings between the ribose protons. His 119 is found in the two complexes in only one conformation, corresponding to position A in the free protein. Side chains of Asn 67, Gln 69, Asn 71, and Glu 111 from transient hydrogen bonds with the adenine base, showing the existence of a pronounced flexibility of these enzyme side chains at the binding site of the downstream adenine. All other general features on the structures coincide clearly with those observed in the crystal state.
[NMR paper] Structure determination of protein/RNA complexes by NMR.
Structure determination of protein/RNA complexes by NMR.
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Methods Enzymol. 2005;394:525-45
Authors: Wu H, Finger LD, Feigon J
Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...
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[NMR paper] Structure determination of protein complexes by NMR.
Structure determination of protein complexes by NMR.
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Methods Mol Biol. 2004;278:255-88
Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED
This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...
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[NMR paper] NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.
NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.
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Biochemistry. 2003 Nov 25;42(46):13541-50
Authors: Sidote DJ, Hoffman DW
A protein component of the Archaeoglobus fulgidus RNase P was expressed in Escherichia coli, purified, and structurally characterized using multidimensional NMR methods. The dominant structural feature of this 11 kDa protein is a sheet of six antiparallel beta-strands, wrapped around a core of conserved...
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[NMR paper] NMR structure of ribonuclease HI from Escherichia coli.
NMR structure of ribonuclease HI from Escherichia coli.
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Biol Pharm Bull. 2000 Oct;23(10):1147-52
Authors: Fujiwara M, Kato T, Yamazaki T, Yamasaki K, Nagayam K
The solution structure of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), a protein of 155 residues, was determined. Three-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) was used to obtain 1,424 distance constraints between individually assigned polypeptide chain hydrogen atoms....
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[NMR paper] The three-dimensional structure of guanine-specific ribonuclease F1 in solution deter
The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry.
Eur J Biochem. 1992 Aug 15;208(1):41-51
Authors: Nakai T, Yoshikawa W, Nakamura H, Yoshida H
Two-dimensional 1H-NMR...
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[NMR paper] 3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to
3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations.
Related Articles 3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations.
J Biomol NMR. 1991 Sep;1(3):283-98
Authors: Rico M, Santoro J, González C, Bruix M, Neira JL, Nieto JL, Herranz J
A method is proposed to generate initial structures in cases where the distance...
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[NMR paper] 3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to
3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations.
Related Articles 3D structure of bovine pancreatic ribonuclease A in aqueous solution: an approach to tertiary structure determination from a small basis of 1H NMR NOE correlations.
J Biomol NMR. 1991 Sep;1(3):283-98
Authors: Rico M, Santoro J, González C, Bruix M, Neira JL, Nieto JL, Herranz J
A method is proposed to generate initial structures in cases where the distance...
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Structure Determination of Protein Complexes by NMR
Structure Determination of Protein Complexes by NMR
D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue
The Department of Biochemistry, University of Cambridge
Introduction
As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...
Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',
Linear Mode
