Abstract:
:The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which contains information about spatially close pairs of protons. Currently, various J-correlated spectra must be recorded in order to obtain the sequence-specific assignments necessary to interpret the NOESY spectra. In this work, a novel procedure to determine the 3D structure and the sequence-specific assignments of a protein using only data from 13C and 15N-separated multidimensional NOESY spectra is described. No information from J-correlated spectra is required. The algorithm is called ANSRS (Assignment of NOESY Spectra in Real Space) and is based on an inversion of the traditional strategy. A 3D real-space structure of detected, but unassigned, 1H spins is calculated from the nuclear Overhauser effect (NOE) distance restraints using a dynamical simulated annealing procedure. The sequence-specific assignments are then determined by searching among the 1H spins in the 3D real-space structure for plausible residue assignments. The search uses a Monte Carlo simulated annealing algorithm based on assignment probabilities derived from the 1H, 15N and 13C chemical shifts, various spatial constraints, and the known sequence of the protein. The procedure has been tested on semi-synthetic data sets comprising published experimental chemical shifts and NOE distance restraints derived from the known 3D structures of the two proteins GAL4 (residues 9 to 41) and bovine pancreatic trypsin inhibitor. The ANSRS procedure was able to determine the sequence-specific assignments for more than 95% of the spins, and was fairly robust with respect to missing NOE data. The potential of the ANSRS approach with respect to automated assignment, reduction of the number of NMR spectra required for a structure determination, assignment of homologous and mutant proteins, and the possibility of analysing spectra recorded at high pH is discussed.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Kraulis PJdoi
10.1016/0022-2836(94)90042-6subject
Has Abstractpub_date
1994-11-04 00:00:00pages
696-718issue
4eissn
0022-2836issn
1089-8638pii
0022-2836(94)90042-6journal_volume
243pub_type
杂志文章abstract::The Holliday junction is the central intermediate in homologous recombination. Branch migration of this four-stranded DNA structure is a key step in genetic recombination that affects the extent of genetic information exchanged between two parental DNA molecules. Here, we have constructed synthetic Holliday junctions ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2001.5408
更新日期:2002-03-08 00:00:00
abstract::The movement of the bacterial insertion sequence IS1 often generates cointegrate structures in which donor and target replicons are connected by direct repeats of IS1. The experiments reported here were designed to understand how IS1 transposition is controlled. Our physical characterization of the structures of coint...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(84)90337-1
更新日期:1984-04-05 00:00:00
abstract::DNA recombinases (RecA in bacteria, Rad51 in eukarya and RadA in archaea) catalyse strand exchange between homologous DNA molecules, the central reaction of homologous recombination, and are among the most conserved DNA repair proteins known. RecA is the sole protein responsible for this reaction in bacteria, whereas ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2009.04.060
更新日期:2009-06-19 00:00:00
abstract::Mutations at solvent-inaccessible core positions in proteins can impact function through many biophysical mechanisms including alterations to thermodynamic stability and protein dynamics. As these properties of proteins are difficult to investigate, the impacts of core mutations on protein function are poorly understo...
journal_title:Journal of molecular biology
pub_type: 评论,杂志文章
doi:10.1016/j.jmb.2013.10.042
更新日期:2014-04-03 00:00:00
abstract::Escherichia coli nitroreductase is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Its ability to convert relatively non-toxic prodrugs such as CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide) into highly cytotoxic derivatives has led to interest in its potential for cancer gene therapy. ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2001.4653
更新日期:2001-05-25 00:00:00
abstract::Rat intestinal fatty-acid-binding protein (I-FABP) is a small (15,124 Mr) cytoplasmic polypeptide that binds long-chain fatty acids in a non-covalent fashion. I-FABP is a member of a family of intracellular binding proteins that are thought to participate in the uptake, transport and/or metabolic targeting of hydropho...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(89)90392-6
更新日期:1989-07-20 00:00:00
abstract::The expression of xylose utilization in Bacillus subtilis is regulated at the level of transcription by xylose dependent Xyl repressor-xyl operator interaction. We have structurally and functionally characterized the binding sites of Xyl repressor in the xyl regulatory region. Methylation and hydroxyl radical protecti...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1669
更新日期:1994-10-28 00:00:00
abstract::Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+ antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the f...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.10.028
更新日期:2006-01-06 00:00:00
abstract::The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specifi...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.1407
更新日期:1994-06-24 00:00:00
abstract::The FLP recombinase of the 2 mu plasmid of Saccharomyces cerevisiae binds to a target containing three 13 base-pair symmetry elements called a, b and c. The symmetry elements b and c are in direct orientation while the a element is in inverted orientation with respect to b and c on the opposite side of an eight base-p...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(05)80320-1
更新日期:1990-11-20 00:00:00
abstract::Type IV pili are multifunctional filaments displayed on many bacterial pathogens. Members of the Type IVa pilus subclass are found on a diverse group of human pathogens, whereas Type IVb pili are found almost exclusively on enteric bacteria. The Type IVa and IVb subclasses are distinguished by differences in the pilin...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2012.02.017
更新日期:2012-04-20 00:00:00
abstract::TWINKLE is the helicase at the mitochondrial DNA (mtDNA) replication fork in mammalian cells. Mutations in the PEO1 gene, which encodes TWINKLE, cause autosomal dominant progressive external ophthalmoplegia (AdPEO), a disorder associated with deletions in mtDNA. Here, we characterized seven different AdPEO-causing mut...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2008.01.035
更新日期:2008-03-28 00:00:00
abstract::Although many putative heme transporters have been discovered, it has been challenging to prove that these proteins are directly involved with heme trafficking in vivo and to identify their heme binding domains. The prokaryotic pathways for cytochrome c biogenesis, Systems I and II, transport heme from inside the cell...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2018.01.022
更新日期:2018-04-13 00:00:00
abstract::Transposable-element-mediated fusion of the conjugal plasmid pOX38::Tn9 with pBR322 results in the appearance of cointegrates composed of a single copy of each plasmid, and cointegrates which carry a single copy of pOX38 but multiple tandem copies of pBR322. These plasmids are separated by directly repeated copies of ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/s0022-2836(83)80249-6
更新日期:1983-03-25 00:00:00
abstract::Caspase recruitment domains (CARDs) are members of the death domain superfamily and contain six antiparallel helices in an alpha-helical Greek key topology. We have examined the equilibrium and kinetic folding of the CARD of Apaf-1 (apoptotic protease activating factor 1), which consists of 97 amino acid residues, at ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.02.105
更新日期:2007-05-25 00:00:00
abstract::Oncogenes may play a crucial role in the genetic program of cellular differentiation; even, probably, at a very early stage in this program, which can be described as pre-commitment. We have investigated the variation in, and the control level of, the accumulation of the transformation-associated cellular protein p53 ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(88)90333-6
更新日期:1988-03-05 00:00:00
abstract::Sir2 is a protein deacetylase that mediates transcriptional silencing at the HM loci, telomeres, and rDNA repeats in yeast. To identify functionally significant regions of the Sir2 protein, we have characterized two types of mutations. First, we used random mutagenesis to create temperature-sensitive alleles of the SI...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.01.044
更新日期:2007-04-13 00:00:00
abstract::Transcription of the repA gene of the Pseudomonas plasmid pPS10 is initiated from a sigma 70 type promoter located 81 bp upstream from the repA gene, extends through the repA gene and the adjacent open reading frame, and ends 1114 nucleotides downstream. The repA promoter is repressed by interactions of the RepA prote...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1994.0134
更新日期:1995-03-24 00:00:00
abstract::We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improved experimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% (R(free) 37.9%) by standard crystallographic methods, a...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.12.031
更新日期:2005-03-04 00:00:00
abstract::We have established a time-resolved fluorescence assay to study fibrillation of the 29 residue peptide hormone glucagon under a variety of different conditions in a high-throughput format. Fibrils formed at pH 2.5 differ in fibrillation kinetics, morphology, thioflavin T staining and FTIR/CD spectra depending on salts...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2005.09.100
更新日期:2006-01-20 00:00:00
abstract::In an X-ray diffraction study using the method of multiple isomorphous replacement, the structure of aspartate carbamoyltransferase (EC 2.1.3.2) complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate (PALA) has been solved to 2.5 A. Ten rounds of model building and 123 cycles of restrained reciprocal spa...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/0022-2836(87)90265-8
更新日期:1987-02-05 00:00:00
abstract::Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs), which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so ma...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2017.02.013
更新日期:2017-04-07 00:00:00
abstract::3'-Uridylylation of RNA is emerging as a phylogenetically widespread phenomenon involved in processing events as diverse as uridine insertion/deletion RNA editing in mitochondria of trypanosomes and small nuclear RNA (snRNA) maturation in humans. This reaction is catalyzed by terminal uridylyltransferases (TUTases), w...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2006.11.065
更新日期:2007-02-23 00:00:00
abstract::Like a variety of other bacteriophages, such as T4 and P22, bacteriophage P1 packages DNA by a "headful" mechanism in which the capacity of the viral capsid determines the size of the single DNA molecule that is packaged. Because of the long-standing and general acceptance of this packaging mechanism, we were surprise...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.1995.0287
更新日期:1995-05-26 00:00:00
abstract::A protein microarray system containing different dilutions of 77 related and non-related proteins was used to show that IgE from subjects allergic to Brazil nut specifically recognise the seed 2S albumin protein (Ber e 1). Further, correctly folded chimaeric 2S albumin proteins containing structural epitope replacemen...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.08.065
更新日期:2004-10-22 00:00:00
abstract::A full length (25,000 base-pair) myosin heavy chain gene completely contained within a single cosmid clone was isolated from a Syrian hamster cosmid genomic library. Sequence comparison of the 3' untranslated region indicated the presence of a 75% homology with the rat embryonic myosin heavy chain gene. Extensive 5' f...
journal_title:Journal of molecular biology
pub_type: 杂志文章,评审
doi:10.1016/0022-2836(91)90251-z
更新日期:1991-04-20 00:00:00
abstract::High amphiphilicity is a hallmark of interfacial helices in membrane proteins and membrane-active peptides, such as toxins and antimicrobial peptides. Although there is general agreement that amphiphilicity is important for membrane-interface binding, an unanswered question is its importance relative to simple hydroph...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2007.05.016
更新日期:2007-07-13 00:00:00
abstract::A series of DNA heptadecamers containing the DNA analogues of RNA E-like 5'-d(GXA)/(AYG)-5' motifs (X/Y is complementary T/A, A/T, C/G, or G/C pair) were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers reveal excellent resolution ...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1006/jmbi.2001.4962
更新日期:2001-09-28 00:00:00
abstract::Interleukin (IL)-12 and IL-23 are heterodimeric proinflammatory cytokines that share a common p40 subunit, paired with p35 and p19 subunits, respectively. They represent an attractive class of therapeutic targets for the treatment of psoriasis and other immune-mediated diseases. Ustekinumab is a fully human monoclonal...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2010.07.046
更新日期:2010-10-08 00:00:00
abstract::We describe light-induced switches for the catalytic activity of the small, RNA-cleaving 8-17 deoxyribozyme (DNAzyme), based on photochemically induced cis-trans isomerization of azobenzene (Az) moieties covalently tethered at various locations within the DNAzyme. Prior studies have shown that trans-azobenzene is able...
journal_title:Journal of molecular biology
pub_type: 杂志文章
doi:10.1016/j.jmb.2004.06.060
更新日期:2004-08-20 00:00:00