Abstract：
:A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore of great interest. However, some of the suboptimal RNA secondary structures computed with classic methods are unsaturated structures, i.e. some structures are included into others. Thus, the incorporation of constraints during the process of folding is not possible, while the incorporation of constraints before the process of folding often introduces a bias into the energy function. This paper describes a new procedure which allows for the incorporation of constraints before and during the process of RNA folding. SAPSSARN is an interactive program which offers a framework, both to specify a secondary structure through a set of folding constraints and to compute all the supoptimal saturated RNA secondary structures which satisfy all the folding constraints. At the start, it relies on the computation of the probabilities of pairing of each base with all others according to McCaskill's algorithm. The constraint satisfaction formulation of the problem deals dynamically with a chosen set of folding constraints and, finally, a search algorithm computes all the suboptimal saturated secondary structures which satisfy those folding constraints. Within such a framework, it is possible to test new ideas about RNA folding and secondary structures, including pseudoknots, can be computed. The program is illustrated with RNA sequences on which we obtained results in agreement with known structures by using a protocol which mimics the hierarchical folding of RNA molecules.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Gaspin C,Westhof Edoi
10.1006/jmbi.1995.0608subject
Has Abstractpub_date
1995-11-24 00:00:00pages
163-74issue
2eissn
0022-2836issn
1089-8638pii
S0022-2836(85)70608-0journal_volume
254pub_type
杂志文章abstract：:Noncoding RNAs (ncRNAs), such as lncRNAs, circRNAs and pri-miRNAs, play important roles in physiological and pathological processes. Recently, it was demonstrated that they could encode proteins or peptides. However, relevant information is scattered across numerous published articles, which is inconvenient for the ex...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.02.022
更新日期：2020-05-15 00:00:00
abstract：:K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2016.11.008
更新日期：2017-02-17 00:00:00
abstract：:A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2001.4739
更新日期：2001-06-22 00:00:00
abstract：:The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recording of three data sets (f'-minimum: 7125 eV, f"-maximum: 7138 eV and r...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1997.1181
更新日期：1997-08-29 00:00:00
abstract：:Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.06.062
更新日期：2005-09-09 00:00:00
abstract：:Here we determined NMR solution structures of two mutants of bovine pancreatic trypsin inhibitor (BPTI) to reveal structural reasons of their decreased thermodynamic stability. A point mutation, A16V, in the solvent-exposed loop destabilizes the protein by 20 degrees C, in contrast to marginal destabilization observed...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(02)00620-4
更新日期：2002-08-23 00:00:00
abstract：:DNA methyltransferases flip their target base out of the DNA helix. Here, we have investigated base flipping by wild-type EcoRV DNA methyltransferase (M.EcoRV) and five M.EcoRV variants (D193A, Y196A, S229A, W231R and Y258A). These variants bind to DNA and S-adenosylmethionine but have a severely reduced catalytic eff...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.2389
更新日期：1999-01-22 00:00:00
abstract：:The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.07.007
更新日期：2005-09-09 00:00:00
abstract：:We have devised a molecular model building computer program (DEZYMER) which builds new ligand binding sites into a protein of known three-dimensional structure. It alters only the sequence and the side-chain structure of the protein, leaving the protein backbone fold intact by definition. The program searches for a co...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90510-d
更新日期：1991-12-05 00:00:00
abstract：:Leech carboxypeptidase inhibitor (LCI) is a 67-residue, tight-binding metallocarboxypeptidase inhibitor composed of a compact domain with a five-stranded beta-sheet and a short alpha-helix that are strongly stabilized by four disulfide bonds. In this study, we investigated the contribution of each particular disulfide...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.06.049
更新日期：2009-09-18 00:00:00
abstract：:Yeast display is a powerful technology for the isolation of monoclonal antibodies (mAbs) against a target antigen. Antibody libraries have been displayed on the surface of yeast as both single-chain variable fragment (scFv) and antigen binding fragment (Fab). Here, we combine these two formats to display well-characte...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.04.019
更新日期：2009-06-05 00:00:00
abstract：:Understanding gene regulation and its adaptive significance requires not only a detailed knowledge of individual molecular interactions that give rise to changes in gene expression but also an overview of complete genetic networks and the ways in which components within them interact. Increasingly, such studies are be...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.06.054
更新日期：2010-09-03 00:00:00
abstract：:Pseudomonas putida uses L-phenylalanine as the sole nitrogen source for growth by converting L-phenylalanine to L-tyrosine, which acts as a donor of the amino group. This metabolic step requires the products of the phhA and phhB genes, which form an operon. Expression of the phhA promoter is mediated by the phhR gene ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2006.12.008
更新日期：2007-03-09 00:00:00
abstract：:Active variant surface glycoprotein (VSG) gene chromatin is preferentially digested by the restriction enzyme HinfI in nuclei of bloodstream variants of Trypanosoma brucei. HinfI sensitivity of VSG gene chromatin is not observed in nuclei of relapse variants in which the VSG gene has been inactivated in situ. Active V...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(87)90559-6
更新日期：1987-10-05 00:00:00
abstract：:The active sites of aspartate transcarbamoylase from Escherichia coli were titrated by measuring the decrease in the enzyme-catalyzed arsenolysis of N-carbamoyl-L-aspartate caused by the addition of the tight-binding inhibitor, N-phosphonacetyl-L-aspartate. Because the enzyme is a poor catalyst for this non-physiologi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(85)90267-0
更新日期：1985-11-05 00:00:00
abstract：:Proteins of the Mob1/phocein family are found in all eukaryotic cells. In yeast, they are activating subunits of Dbf2-related protein kinases involved in cell cycle control. Despite the wide occurrence of these proteins, their biological functions remain poorly understood. Here we report the solution structure of the ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.01.010
更新日期：2004-03-12 00:00:00
abstract：:Dengue virus (DV) infection depends on a step of membrane fusion, which occurs in the acidic environment of the endosome. This process is mediated by virus surface envelope glycoprotein, in which the loop between residues D98-G112 is considered to be crucial, acting as a fusion peptide. Here, we have characterized fun...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2009.07.035
更新日期：2009-09-25 00:00:00
abstract：:Crystals of a relatively unspecific NAD(P)H dehydrogenase from human erythrocytes suitable for X-ray analysis have been grown. They belong to space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2 with unit cell dimensions: a = b = 79.3 A and c = 38.1 A. The asymmetric unit contains one molecule of Mr 18,000. ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90093-7
更新日期：1984-04-25 00:00:00
abstract：:Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleot...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2013.10.036
更新日期：2014-02-06 00:00:00
abstract：:The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens su...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2019.04.002
更新日期：2019-08-23 00:00:00
abstract：:The innermost chorionic layer (ICL) within egg shells of Drosophila melanogaster is composed of thin, abutting three-dimensional crystalline plates which form a closed, membrane-like sheath. Collectively, the crystals within the sheath appear to form a family of related three-dimensional crystals in space group C222; ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(87)90350-0
更新日期：1987-02-20 00:00:00
abstract：:The chemotactic cytokine RANTES (Regulated on Activation, Normal T-cell Expressed and Secreted) is a potent chemoattractant and activator of a number of leukocytes, with a molecular mass of 8 kDa. Crystals of this protein have been grown from 100 mM sodium acetate buffer (pH 4.6) containing 200 mM magnesium acetate, w...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1605
更新日期：1994-09-30 00:00:00
abstract：:The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested tha...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.02.031
更新日期：2020-03-27 00:00:00
abstract：:Steroids and retinoids are signaling molecules that control a variety of physiological processes. 17beta-Hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyzes the reduction of estrone to estradiol, supplying biologically active estrogen-regulating sex-specific differentiation. Photoreceptor-associated retinol de...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.04.002
更新日期：2010-06-04 00:00:00
abstract：:The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage phi29 virus capsid. On the basis of the results of single-molecule experimental studies, we propose a push and roll mechanism to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while rotati...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.05.002
更新日期：2010-07-09 00:00:00
abstract：:The replacement of cis proline 39 of ribonuclease T1 by an alanine residue leads to a decrease in stability by about 20 kJ/mol and to major changes in the folding kinetics that are not easily explained by the proline model for protein folding. In particular, a novel very slow reaction is observed in the refolding of t...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1337
更新日期：1993-06-05 00:00:00
abstract：:Auxin is a plant hormone that is central to plant growth and development from embryogenesis to senescence. Auxin signaling is mediated by auxin response transcription factors (ARFs) and Aux/IAA repressors that regulate the expression of a multitude of auxin response genes. ARF and Aux/IAA proteins assemble into homome...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.04.007
更新日期：2020-06-26 00:00:00
abstract：:Mimivirus is the largest known virus. Using cryo-electron microscopy, the virus was shown to be icosahedral, covered by long fibers, and appears to have at least two lipid membranes within its protein capsid. A unique vertex, presumably for attachment and infection of the host, can be seen for particles that have a su...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.08.060
更新日期：2005-10-28 00:00:00
abstract：:A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear an...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.12.037
更新日期：2005-03-04 00:00:00
abstract：:Binary complexes between messenger RNA and E. coli ribosomes were examined. A ribosome-mRNA binary complex on T4 gene 32 mRNA withstood inhibition by antibodies against ribosomal protein S1. Anti-S1 blocks ternary complex formation, as measured by "extension inhibition" or "toeprinting" analysis, only when preincubate...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(91)90876-8
更新日期：1991-03-05 00:00:00
