Structure-based analysis of protein-RNA interactions using the program ENTANGLE

Allers, Jim; Shamoo, Yousif

doi:10.1006/jmbi.2001.4857

Cited by 227 publications

(261 citation statements)

References 63 publications

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“…The strongest effects were caused by mutations of amino acids that altered the interaction of YS11 with nucleotides either in KT-11 or in the terminal loop of H11, results that are consistent with and complement an earlier determination of the identity elements in 18 S rRNA (20 (20). With few exceptions, ribosomal proteins are dominated by basic amino acids, and they are often involved in RNA recognition (29,30). Of the nine amino acids in YS11 that were required for binding to rRNA, six are basic.…”

Section: Contribution Of Amino Acids In Ys11 Tosupporting

confidence: 83%

Determination of the Amino Acids in Yeast Ribosomal Protein YS11 Essential for the Recognition of Nucleotides in 18 S Ribosomal RNA

Dresios¹,

Chan

Wool

2006

Journal of Biological Chemistry

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Section: Contribution Of Amino Acids In Ys11 Tosupporting

confidence: 83%

Determination of the Amino Acids in Yeast Ribosomal Protein YS11 Essential for the Recognition of Nucleotides in 18 S Ribosomal RNA

Dresios¹,

Chan

Wool

2006

Journal of Biological Chemistry

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“…The use of the less specific protease, Proteinase K, resulted in 11 more completely digested proteins as compared to trypsin. Such results are to be expected given the lack of specificity for Proteinase K. However, because interactions between r-proteins and rRNA are usually through salt-bridges between positively charged residues on the proteins and phosphate oxygen atoms on the RNA [41], basic residues such as arginine and lysine that interact with rRNA through salt-bridges will be less susceptible to proteolysis. Thus, protease specificity may not account for all of the differences between trypsin and Proteinase K found in this study, although an examination of the data obtained in this study did not discern any relationship between the frequency of Arg/Lys residues within a protein and the rate of proteolysis with trypsin.…”

Section: Comparison Of E Coli Maldi-ms Data Obtained From Different mentioning

confidence: 96%

Developing limited proteolysis and mass spectrometry for the characterization of ribosome topography

Suh

Pourshahian

Limbach

2007

J. Am. Soc. Mass Spectrom.

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An approach that combines limited proteolysis and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been developed to probe protease-accessible sites of ribosomal proteins from intact ribosomes. Escherichia coli and Thermus thermophilus 70S ribosomes were subjected to limited proteolysis using different proteases under strictly controlled conditions. Intact ribosomal proteins and large proteolytic peptides were recovered and directly analyzed by MALDI-MS, which allows for the determination of proteins that are resistant to proteolytic digestion by accurate measurement of molecular weights. Larger proteolytic peptides can be directly identified by the combination of measured mass, enzyme specificity and protein database searching. Sucrose density gradient centrifugation revealed that the majority of the 70S ribosome dissociates into intact 30S and 50S subunits after 120 min of limited proteolysis. Thus, examination of ribosome populations within the first 30-60 min of incubation provide insight into 70S structural features. Results from E. coli and T. thermophilus revealed that a significantly larger fraction of 50S ribosomal proteins have similar limited proteolysis behavior than the 30S ribosomal proteins of these two organisms. The data obtained by this approach correlate with information available from the high resolution crystal structures of both organisms. This new approach will be applicable to investigations of other large ribonucleoprotein complexes, is readily extendable to ribosomes from other organisms, and can facilitate additional structural studies on ribosome assembly intermediates.The ribosome, found in all organisms, is the subcellular organelle that performs the activity of protein synthesis. Prokaryotic ribosomes, which sediment at 70S, have a molecular mass of approximately 2.5 ×10 6 Da and consist of two subunits, the 50S and the 30S. Each subunit has a unique number of proteins and ribosomal RNAs (rRNAs). Eukaryotic ribosomes, which sediment at 80S, are substantially larger and more complex than their prokaryotic counterparts. Two subunits, the 60S and 40S, together contain at least 78 unique proteins and 4 rRNAs. The small subunit binds messenger RNA (mRNA) and mediates the interactions between mRNA and transfer RNAs (tRNAs). The larger subunit catalyzes peptide-bond formation. During the initiation phase of protein synthesis, the two subunits behave independently, assembling into complete ribosomes only when elongation is about to begin.A fundamental prerequisite for understanding the biochemical interactions occurring within the ribosome during protein synthesis is a detailed knowledge of the structure of this † Current address: Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10021 * To whom correspondence should be addressed. Phone (513) 556-1871, Fax (513) Email: Pat.Limbach@uc.edu Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to ou...

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“…The base is sandwiched in a pocket between the side chains of Phe-37 (from loop ␤1-␤2) and His-112 (of helix ␣4) at a distance of 3.4 Å to each (Fig. 3A); such a parallel ring stacking between bases and aromatic residues is typical for protein-nucleic acid interactions (28). A series of hydrogen bonds to the base are observed: between the mainchain atoms of Phe-37 and the base ring of the nucleotide, from the side chain of Gln-36, from the side chain of Asn-115 # of a symmetry-related molecule and a water-mediated hydrogen bond to Asn-39 N, and the side chain of Asn 115 # (Fig.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties

Neumann¹,

Lieber²,

Meyer³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Structure-based analysis of protein-RNA interactions using the program ENTANGLE

Cited by 227 publications

References 63 publications

Determination of the Amino Acids in Yeast Ribosomal Protein YS11 Essential for the Recognition of Nucleotides in 18 S Ribosomal RNA

Determination of the Amino Acids in Yeast Ribosomal Protein YS11 Essential for the Recognition of Nucleotides in 18 S Ribosomal RNA

Developing limited proteolysis and mass spectrometry for the characterization of ribosome topography

Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties

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