Effects of experimentally achievable improvements in the quality of NMR distance constraints on the accuracy of calculated protein structures.


:New methods for collecting cross-relaxation data from proteins and nucleic acids make it possible to improve the accuracy and precision of interproton distance measurements used as input for NMR solution structure determinations. It thus is of interest to determine whether such experimentally achievable improvements in input distance constraints have significant effects on the precision and accuracy of the resulting structures. To answer this question, we have turned to a computational procedure involving the use of data simulated from a known structure, in order to allow unambiguous assessments of accuracy. The approach to improved distances evaluated here is that afforded by magnetization exchange network editing (MENE); MENE pulse sequences break the network of cross-relaxation interactions into regions that are manipulated so as to defeat certain spin-diffusion terms. A target structure was prepared from the X-ray structure of a small protein, turkey ovomucoid third domain (OMTKY3). A normal NOESY spectrum and two varieties of MENE spectra, BD-NOESY and CBD-NOESY, were simulated by means of complete relaxation matrix analysis. These results were used to create different input data sets with the same number of constraints (perfectly accurate distances derived from the target structure, more accurate distances derived from the MENE simulations, and less accurate distances derived from the NOESY simulation), and these, interpreted at different levels of precision, were used as input for solution structure calculations. The results showed that the use of more precise input data measurably improves the local precision and accuracy of calculated structures, but only if the more precise data include the actual target distance. Incorporation of the experimentally achievable, accurate distances with higher precision afforded by the MENE pulse sequences into the set of input distances was found to improve the accuracy of the resulting structures, particularly in terms of side-chain conformation.


J Mol Biol


Hoogstraten CG,Markley JL




Has Abstract


1996-05-03 00:00:00














  • Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution.

    abstract::The structure of basic Winged Bean Agglutinin (WBAI) with two dimeric molecules complexed with methyl-alpha-D-galactopyranoside in the asymmetric unit, has been determined by the molecular replacement method and refined with 2.5 A X-ray intensity data. The polypeptide chain of each monomer has the characteristic legum...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Prabu MM,Sankaranarayanan R,Puri KD,Sharma V,Surolia A,Vijayan M,Suguna K

    更新日期:1998-03-06 00:00:00

  • ATP synthase from bovine heart mitochondria. In vitro assembly of a stalk complex in the presence of F1-ATPase and in its absence.

    abstract::Four subunits of the F1F0-ATPase from bovine heart mitochondria have been produced by heterologous over-expression in Escherichia coli. They are the oligomycin sensitivity conferral protein (OSCP), coupling factor 6 (F6) and subunits b and d. Likewise, fragments b', bI, bC, and bM (amino acid residues 79 to 214, 121 t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Collinson IR,van Raaij MJ,Runswick MJ,Fearnley IM,Skehel JM,Orriss GL,Miroux B,Walker JE

    更新日期:1994-09-30 00:00:00

  • The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death.

    abstract::Antidote/toxin gene pairs known as "addiction modules" can maintain plasmids in bacterial populations by means of post-segregational killing. However, several chromosome-encoded addiction modules may provide an entirely distinct function in the programmed cell death of moribund subpopulations under starvation conditio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Bishop RE,Leskiw BK,Hodges RS,Kay CM,Weiner JH

    更新日期:1998-07-24 00:00:00

  • The 80's loop (residues 78 to 85) is important for the differential activity of retroviral proteases.

    abstract::The abundance of structural data available for retroviral proteases affords a unique opportunity to investigate structure activity relationships. Our approach attempts to genetically engineer an HIV (human immunodeficiency virus)-1 protease that is functionally equivalent to the HIV-2 and the SIV (simian immunodeficie...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Stebbins J,Towler EM,Tennant MG,Deckman IC,Debouck C

    更新日期:1997-04-04 00:00:00

  • Telomeric Transcription and Telomere Rearrangements in Quiescent Cells.

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Coulon S,Vaurs M

    更新日期:2020-07-10 00:00:00

  • Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation.

    abstract::The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Li AY,Lee J,Borek D,Otwinowski Z,Tibbits GF,Paetzel M

    更新日期:2011-10-28 00:00:00

  • Kinetic models for unfolding and refolding of ribonuclease T1 with substitution of cis-proline 39 by alanine.

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mayr LM,Schmid FX

    更新日期:1993-06-05 00:00:00

  • Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties.

    abstract::Pancreatic amyloid is found in more than 95 % of type II diabetes patients. Pancreatic amyloid is formed by the aggregation of islet amyloid polypeptide (hIAPP or amylin), which is a 37-residue peptide. Because pancreatic amyloid is cytotoxic, it is believed that its formation is directly associated with the developme...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tenidis K,Waldner M,Bernhagen J,Fischle W,Bergmann M,Weber M,Merkle ML,Voelter W,Brunner H,Kapurniotu A

    更新日期:2000-01-28 00:00:00

  • The structure of the Sec13/31 COPII cage bound to Sec23.

    abstract::Structural studies have revealed some of the organizing principles and mechanisms involved in the assembly of the COPII coat including the location of the Sec23/24 adapter layer. Previous studies, however, were unable to unambiguously determine the positions of Sec23 and Sec24 in the coat. Here, we have determined a c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Bhattacharya N,O Donnell J,Stagg SM

    更新日期:2012-07-20 00:00:00

  • Tandemly repeated DNA sequences from Xenopus laevis. II. Dispersed clusters of a 388 base-pair repeating unit.

    abstract::A repetitive DNA sequence family from Xenopus laevis that has an unusual genomic organization has been identified. It has been shown by blot-hybridization that this sequence occurs in clusters containing variable numbers of the 388 base-pair repeating unit. There are approximately 500 such clusters in the genome, and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lam BS,Carroll D

    更新日期:1983-04-25 00:00:00

  • In vitro DNA tethering of HIV-1 integrase by the transcriptional coactivator LEDGF/p75.

    abstract::Although LEDGF/p75 is believed to act as a cellular cofactor of lentiviral integration by tethering integrase (IN) to chromatin, there is no good in vitro model to analyze this functionality. We designed an AlphaScreen assay to study how LEDGF/p75 modulates the interaction of human immunodeficiency virus type 1 IN wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: McNeely M,Hendrix J,Busschots K,Boons E,Deleersnijder A,Gerard M,Christ F,Debyser Z

    更新日期:2011-07-29 00:00:00

  • Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution.

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hall MD,Levitt DG,Banaszak LJ

    更新日期:1992-08-05 00:00:00

  • Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II).

    abstract::The methyltransferase RlmA(II) (formerly TlrB) is found in many Gram-positive bacteria, and methylates the N-1 position of nucleotide G748 within the loop of hairpin 35 in 23S rRNA. Methylation of the rRNA by RlmA(II) confers resistance to tylosin and other mycinosylated 16-membered ring macrolide antibiotics. We have...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lebars I,Husson C,Yoshizawa S,Douthwaite S,Fourmy D

    更新日期:2007-09-14 00:00:00

  • Three-dimensional structure of the wild-type lac Pribnow promoter DNA in solution. Two-dimensional nuclear magnetic resonance studies and distance geometry calculations.

    abstract::The solution structure of a 12 base-pair DNA duplex containing the wt-lac promoter Pribnow sequence TATGTT has been studied by two-dimensional nuclear magnetic resonance spectroscopy. Proton assignments for the 24 sugar and base residues were obtained from two-dimensional correlated nuclear magnetic resonance and two-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Nerdal W,Hare DR,Reid BR

    更新日期:1988-06-20 00:00:00

  • Structure of a Ca(2+)/CaM:Kv7.4 (KCNQ4) B-helix complex provides insight into M current modulation.

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    pub_type: 杂志文章


    authors: Xu Q,Chang A,Tolia A,Minor DL Jr

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  • Targeted Killing of Pseudomonas aeruginosa by Pyocin G Occurs via the Hemin Transporter Hur.

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  • Expanding the Chemogenetic Toolbox by Circular Permutation.

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    authors: Nyon MP,Rice DW,Berrisford JM,Hounslow AM,Moir AJ,Huang H,Nathan S,Mahadi NM,Bakar FD,Craven CJ

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lescure A,Tebb G,Mattaj IW,Krol A,Carbon P

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    pub_type: 杂志文章


    authors: Mittermaier A,Varani L,Muhandiram DR,Kay LE,Varani G

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Foloppe N,Sagemark J,Nordstrand K,Berndt KD,Nilsson L

    更新日期:2001-07-06 00:00:00

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    authors: Cagliani R,Forni D,Tresoldi C,Pozzoli U,Filippi G,Rainone V,De Gioia L,Clerici M,Sironi M

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    pub_type: 杂志文章


    authors: Gógl G,Biri-Kovács B,Durbesson F,Jane P,Nomine Y,Kostmann C,Bilics V,Simon M,Reményi A,Vincentelli R,Trave G,Nyitray L

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Pham CL,Leong SL,Ali FE,Kenche VB,Hill AF,Gras SL,Barnham KJ,Cappai R

    更新日期:2009-04-03 00:00:00

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wan WY,Milner-White EJ

    更新日期:1999-03-12 00:00:00

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: McLachlan AD

    更新日期:1983-09-05 00:00:00

  • Myosin binding surface on actin probed by hydroxyl radical footprinting and site-directed labels.

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    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Oztug Durer ZA,Kamal JK,Benchaar S,Chance MR,Reisler E

    更新日期:2011-11-25 00:00:00