当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Consensus protein design without phylogenetic bias.

Consensus protein design without phylogenetic bias.

Abstract：

:Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a single protein represents a reliable alternative source of sequence diversity that is essentially free of phylogenetic bias. A small number of functional protein sequences selected from binary-patterned libraries suffice as input for the consensus design of active enzymes that are easier to produce and substantially more stable than individual members of the starting data set. Although catalytic activity correlates less consistently with sequence conservation in these extensively randomized proteins, less extreme mutagenesis strategies might be adopted in practice to augment stability while maintaining function.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Jäckel C,Bloom JD,Kast P,Arnold FH,Hilvert D

doi

10.1016/j.jmb.2010.04.039

subject

Has Abstract

pub_date

2010-06-18 00:00:00

pages

541-6

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(10)00427-4

journal_volume

399

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Crystallization and preliminary X-ray studies of a protease from Pseudomonas aeruginosa.

    abstract：:A protease produced by Pseudomonas aeruginosa has been crystallized by the vapor-diffusion method using polyethylene glycol 4000 as a precipitant. The crystals belong to the hexagonal space group P6(1) (P6(5) with unit cell dimensions; a = b = 106.9 A, c = 96.9 A. There are two molecules per asymmetric unit. The cryst...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1247

    authors： Harada S,Nagara A,Kurisu G,Kai Y

    更新日期：1993-04-20 00:00:00

  • Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association.

    abstract：:A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be e...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90262-i

    authors： Wolfe AR,Meehan T

    更新日期：1992-02-20 00:00:00

  • Identification of a minimal binding element within the T7 RNA polymerase promoter.

    abstract：:The T7 RNA polymerase promoter has been proposed to contain two domains: the binding region upstream of position -5 is recognized through apparently traditional duplex contacts, while the catalytic domain downstream of position -5 is bound in a melted configuration. This model is tested by following polymerase binding...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1350

    authors： Ujvári A,Martin CT

    更新日期：1997-11-07 00:00:00

  • Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.

    abstract：:Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease. Here we present Galaxy InteractoMIX (http://galaxy.interactomix.com), a platform composed of 13 different computational tools each addressing specific ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.09.015

    authors： Mirela-Bota P,Aguirre-Plans J,Meseguer A,Galletti C,Segura J,Planas-Iglesias J,Garcia-Garcia J,Guney E,Oliva B,Fernandez-Fuentes N

    更新日期：2020-09-23 00:00:00

  • Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution.

    abstract：:The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90285-2

    authors： Bolognesi M,Coda A,Gatti G,Ascenzi P,Brunori M

    更新日期：1985-05-05 00:00:00

  • NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.

    abstract：:The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.03.041

    authors： Fadeev EA,Sam MD,Clubb RT

    更新日期：2009-05-15 00:00:00

  • Immunity repressor of bacteriophage P2. Identification and DNA-binding activity.

    abstract：:The product of gene C of the temperate bacteriophage P2, the immunity repressor, can be detected as a unique band eluting from phosphocellulose columns at 0.12 M-potassium phosphate when differentially labelled with a radioactive amino acid: the band is absent when phages that either have lost gene C through deletion ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90242-0

    authors： Lundqvist B,Bertani G

    更新日期：1984-09-25 00:00:00

  • Human transcriptional coactivator PC4 stimulates DNA end joining and activates DSB repair activity.

    abstract：:Human transcriptional coactivator PC4 is a highly abundant nuclear protein that is involved in diverse cellular processes ranging from transcription to chromatin organization. Earlier, we have shown that PC4, a positive activator of p53, overexpresses upon genotoxic insult in a p53-dependent manner. In the present stu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.11.008

    authors： Batta K,Yokokawa M,Takeyasu K,Kundu TK

    更新日期：2009-01-23 00:00:00

  • Celastrol inhibits Tat-mediated human immunodeficiency virus (HIV) transcription and replication.

    abstract：:Current drugs used for antiretroviral therapy against human immunodeficiency virus (HIV) have a narrow spectrum of activity and, more often, have associated toxicities and severe side effects in addition to developing resistance. Thus, there is a need to develop new therapeutic strategies against HIV/AIDS to complemen...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.04.013

    authors： Narayan V,Ravindra KC,Chiaro C,Cary D,Aggarwal BB,Henderson AJ,Prabhu KS

    更新日期：2011-07-29 00:00:00

  • Identification and sequence analysis of a silent gene (ushA0) in Salmonella typhimurium.

    abstract：:The evolution of new or improved enzyme specificities in prokaryotes has been proposed to involve gene duplication, followed by silencing of one of the duplicates at the transcriptional or translational level. Such "silent gene intermediates" are distinct from "cryptic" genes, which are proposed to have a different ro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90358-x

    authors： Burns DM,Beacham IR

    更新日期：1986-11-20 00:00:00

  • Peptide mimic of the HIV envelope gp120-gp41 interface.

    abstract：:The human immunodeficiency virus envelope glycoprotein (Env) is composed of surface (gp120) and transmembrane (gp41) subunits, which are noncovalently associated on the viral surface. Human immunodeficiency virus Env mediates viral entry after undergoing a complex series of conformational changes induced by interactio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.12.001

    authors： Kim S,Pang HB,Kay MS

    更新日期：2008-02-22 00:00:00

  • Calcium-dependent homoassociation of E-cadherin by NMR spectroscopy: changes in mobility, conformation and mapping of contact regions.

    abstract：:Cadherins are calcium-dependent cell surface proteins that mediate homophilic cellular adhesion. The calcium-induced oligomerization of the N-terminal two domains of epithelial cadherin (ECAD12) was followed by NMR spectroscopy in solution over a large range of protein (10 microM-5 mM) and calcium (0-5 mM) concentrati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01137-3

    authors： Häussinger D,Ahrens T,Sass HJ,Pertz O,Engel J,Grzesiek S

    更新日期：2002-12-06 00:00:00

  • Transition of chromatin from the "10 nm" lower order structure, to the "30 nm" higher order structure as followed by small angle X-ray scattering.

    abstract：:Chromatin oligomers undergo a conformational change from a "10 nm" lower order structure at low concentration of salt to a "30 nm" higher order structure, with increasing NaCl or MgCl2 concentration. We have extended our previously reported hydrodynamic and light-scattering measurements of the folding of well-defined ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90353-6

    authors： Greulich KO,Wachtel E,Ausio J,Seger D,Eisenberg H

    更新日期：1987-02-20 00:00:00

  • Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli.

    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

    authors： Kedrov A,Janovjak H,Ziegler C,Kuhlbrandt W,Muller DJ

    更新日期：2006-01-06 00:00:00

  • Structural studies of HIV-1 Tat protein.

    abstract：:Tat (trans-activator) proteins are early RNA binding proteins regulating lentiviral transcription. These proteins are necessary components in the life cycle of all known lentiviruses, such as the human immunodeficiency viruses (HIV) or the equine infectious anemia virus (EIAV). Tat proteins are thus ideal targets for ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0158

    authors： Bayer P,Kraft M,Ejchart A,Westendorp M,Frank R,Rösch P

    更新日期：1995-04-07 00:00:00

  • Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.

    abstract：:HtrA (high-temperature requirement A) family proteins play important roles in protein-quality control processes in the bacterial periplasm. A common feature of all members of this family is their modular organization comprising a chymotrypsin-like protease domain and at least one PDZ (postsynaptic density of 95 kDa, d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.06.023

    authors： Schubert A,Wrase R,Hilgenfeld R,Hansen G

    更新日期：2015-08-28 00:00:00

  • DBC2 is essential for transporting vesicular stomatitis virus glycoprotein.

    abstract：:DBC2 is a tumor suppressor gene linked to breast and lung cancers. Although DBC2 belongs to the RHO GTPase family, it has a unique structure that contains a Broad-Complex/Tramtrack/Bric a Brac (BTB) domain at the C terminus instead of a typical CAAX motif. A limited number of functional studies on DBC2 have indicated ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.09.026

    authors： Chang FK,Sato N,Kobayashi-Simorowski N,Yoshihara T,Meth JL,Hamaguchi M

    更新日期：2006-12-01 00:00:00

  • Requirement of 3'-terminal guanosine in (-)-stranded RNA for in vitro replication of cucumber mosaic virus satellite RNA by viral RNA-dependent RNA polymerase.

    abstract：:The 3' terminus of the (-) RNA strand in the replicative forms of several (+)-stranded RNA viruses possesses an unpaired guanosine with unknown function. This unpaired guanosine is also found at the 3' terminus of the (-) strand in the double-stranded form of two cucumoviral satellite RNAs. Using a cucumber mosaic vir...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1326

    authors： Wu G,Kaper JM

    更新日期：1994-05-20 00:00:00

  • In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

    abstract：:Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mamm...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.05.014

    authors： Czudnochowski N,Wang AL,Finer-Moore J,Stroud RM

    更新日期：2013-10-23 00:00:00

  • Stability of a homo-dimeric Ca(2+)-binding member of the beta gamma-crystallin superfamily: DSC measurements on spherulin 3a from Physarum polycephalum.

    abstract：:Spherulin 3a (S3a) from Physarum polycephalum represents the only known single-domain member of the superfamily of beta gamma eye-lens crystallins. It shares the typical two Greek-key motif and is stabilized by dimerization and Ca(2+)-binding. The temperature and denaturant-induced unfolding of S3a in the absence and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3037

    authors： Kretschmar M,Jaenicke R

    更新日期：1999-09-03 00:00:00

  • Rigidification of a flexible protease inhibitor variant upon binding to trypsin.

    abstract：:The Tyr35-->Gly replacement in bovine pancreatic trypsin inhibitor (BPTI) has previously been shown to dramatically enhance the flexibility of the trypsin-binding region of the free inhibitor and to destabilize the interaction with the protease by about 3 kcal/mol. The effects of this replacement on the enzyme-inhibit...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.003

    authors： Hanson WM,Domek GJ,Horvath MP,Goldenberg DP

    更新日期：2007-02-09 00:00:00

  • Preliminary X-ray studies on an unspecific NAD(P)H dehydrogenase from human erythrocytes.

    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

    authors： Pai EF

    更新日期：1984-04-25 00:00:00

  • Transcriptional control in the EcoRI-F immunity region of Bacillus subtilis phage phi 105. Identification and unusual structure of the operator.

    abstract：:We present the first evidence, in Bacillus subtilis, for gene regulation through the classical mechanism of repressor-operator interaction. The EcoRI-F immunity region (immF) of lysogenic phage phi 105 contains two promoters, PM and PR, in divergent orientations. PM initiates transcription of the phi 105 repressor (c ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90609-7

    authors： Van Kaer L,Van Montagu M,Dhaese P

    更新日期：1987-09-05 00:00:00

  • Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

    abstract：:A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90932-a

    authors： Kidera A,Go N

    更新日期：1992-05-20 00:00:00

  • Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response.

    abstract：:In the early stages of infection, gaining control of the cellular protein synthesis machinery including its ribosomes is the ultimate combat objective for a virus. To successfully replicate, viruses unequivocally need to usurp and redeploy this machinery for translation of their own mRNA. In response, the host trigger...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.04.040

    authors： Hoang HD,Graber TE,Alain T

    更新日期：2018-07-06 00:00:00

  • Involvement of the domains of histones H1 and H5 in the structural organization of soluble chromatin.

    abstract：:We have studied in reconstitution experiments the conditions under which peptides derived from histones H1 and H5 are bound in chromatin and to what extent they are involved in the organization of chromatin fibers. The fragments of rat liver histone H1 (rH1) and chicken erythrocytes H1 (cH1) and H5 (cH5) used were the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80102-8

    authors： Thoma F,Losa R,Koller T

    更新日期：1983-07-05 00:00:00

  • Isolation of proteins that interact with the signal transduction molecule Dof and identification of a functional domain conserved between Dof and vertebrate BCAP.

    abstract：:Dof is a large molecule essential for signal transduction by the two FGF receptors in Drosophila. It contains two ankyrin repeats and a coiled-coil region, but has no other recognisable structural motif. Dof shares these features with its closest vertebrate relatives, the B-cell signalling molecules BCAP and BANK. In ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00489-3

    authors： Battersby A,Csiszár A,Leptin M,Wilson R

    更新日期：2003-06-06 00:00:00

  • FlgB, FlgC, FlgF and FlgG. A family of structurally related proteins in the flagellar basal body of Salmonella typhimurium.

    abstract：:The flagellar basal body of Salmonella typhimurium consists of four rings surrounding a rod. The rod, which is believed to transmit motor rotation to the filament, is not well characterized in terms of its structure and composition. FlgG is known to lie within the distal portion of the rod, in the region where it is s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90365-S

    authors： Homma M,Kutsukake K,Hasebe M,Iino T,Macnab RM

    更新日期：1990-01-20 00:00:00

  • The Third Coiled Coil Domain of Atg11 Is Required for Shaping Mitophagy Initiation Sites.

    abstract：:Selective autophagy is the capture of specific cytosolic contents in double-membrane vesicles that subsequently fuse with the vacuole or lysosome, thereby delivering cargo for degradation. Selective autophagy receptors (SARs) mark the cargo for degradation and, in yeast, recruit Atg11, the scaffolding protein for sele...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.08.025

    authors： Margolis HK,Katzenell S,Leary KA,Ragusa MJ

    更新日期：2020-10-02 00:00:00

  • prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli.

    abstract：:Toxin-antitoxin systems consist of a stable toxin, frequently with endonuclease activity, and a small, labile antitoxin, which sequesters the toxin into an inactive complex. Under unfavorable conditions, the antitoxin is degraded, leading to activation of the toxin and resulting in growth arrest, possibly also in bact...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.016

    authors： Schmidt O,Schuenemann VJ,Hand NJ,Silhavy TJ,Martin J,Lupas AN,Djuranovic S

    更新日期：2007-09-28 00:00:00