Evolvability of thermophilic proteins from archaea and bacteria.

Abstract:

:Proteins from thermophiles possess high thermostability. The stabilization mechanisms differ between archaeal and bacterial proteins, whereby archaeal proteins are mainly stabilized via hydrophobic interactions and bacterial proteins by ion pairs. High stability is an important factor in promoting protein evolution, but the precise means by which different stabilization mechanisms affect the evolution process remain unclear. In this study, we investigated a random mutational drift of esterases from thermophilic archaea and bacteria at high temperatures. Our results indicate that mutations in archaeal proteins lead to improved function with no loss of stability, while mutant bacterial proteins are largely destabilized with decreased activity at high temperatures. On the basis of these findings, we suggest that archaeal proteins possess higher "evolvability" than bacterial proteins under temperature selection and are additionally able to evolve into eukaryotic proteins.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Takano K,Aoi A,Koga Y,Kanaya S

doi

10.1021/bi400652c

subject

Has Abstract

pub_date

2013-07-16 00:00:00

pages

4774-80

issue

28

eissn

0006-2960

issn

1520-4995

journal_volume

52

pub_type

杂志文章
  • Carboxylate ions are strong allosteric ligands for the HisB10 sites of the R-state insulin hexamer.

    abstract::The insulin hexamer is an allosteric protein which displays positive and negative cooperativity and half-site reactivity that is modulated by strong homotropic and heterotropic ligand binding interactions at two different loci. These loci consist of phenolic pockets situated on the dimer-dimer interfaces of T-R and R-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9701639

    authors: Huang ST,Choi WE,Bloom C,Leuenberger M,Dunn MF

    更新日期:1997-08-12 00:00:00

  • EGF-mCherry Fusion Protein Expressed in E. coli Shows Product Heterogeneity but a High Biological Activity.

    abstract::The epidermal growth factor receptor (EGFR) is a transmembrane protein involved in cell signaling processes, and dysregulation of its activity often drives tumor growth. EGFR is a clinically validated tumor marker and target for antibodies and tyrosine kinase inhibitors. We demonstrate that a fusion protein of the nat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.9b00021

    authors: Feiner RC,Pennè I,Müller B,Müller KM

    更新日期:2019-02-26 00:00:00

  • Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin.

    abstract::The thermodynamic binding parameters and crystal structure for streptavidin-peptide complexes where the peptide sequences were obtained by random screening methods are reported. The affinities between streptavidin and two heptapeptides were determined by titrating calorimetric methods [Phe-Ser-His-Pro-Gln-Asn-Thr, Ka ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00154a004

    authors: Weber PC,Pantoliano MW,Thompson LD

    更新日期:1992-10-06 00:00:00

  • Expression and Purification of ZASP Subdomains and Clinically Important Isoforms: High-Affinity Binding to G-Actin.

    abstract::Z-disc-associated, alternatively spliced, PDZ motif-containing protein (ZASP) is a principal component of the sarcomere. The three prevalent isoforms of ZASP in skeletal muscle are generated by alternative splicing of exons 9 and 10. The long isoforms, either having (ZASP-L) or lacking exon 10 (ZASP-LΔex10), include a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00067

    authors: Watts NR,Zhuang X,Kaufman JD,Palmer IW,Dearborn AD,Coscia S,Blech-Hermoni Y,Alfano C,Pastore A,Mankodi A,Wingfield PT

    更新日期:2017-04-11 00:00:00

  • Profiling Aglycon-Recognizing Sites of UDP-glucose:glycoprotein Glucosyltransferase by Means of Squarate-Mediated Labeling.

    abstract::Because of its ability to selectively glucosylate misfolded glycoproteins, UDP-glucose:glycoprotein glucosyltransferase (UGGT) functions as a folding sensor in the glycoprotein quality control system in the endoplasmic reticulum (ER). The unique property of UGGT derives from its ability to transfer a glucose residue t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00785

    authors: Ohara K,Takeda Y,Daikoku S,Hachisu M,Seko A,Ito Y

    更新日期:2015-08-11 00:00:00

  • Electron-transfer reactions in manganese-depleted photosystem II.

    abstract::We have used flash-detection optical and electron paramagnetic resonance spectroscopy to measure the kinetics and yield per flash of the photooxidation of cytochrome b559 and the yield per flash of the photooxidation of the tyrosine residue YD in Mn-depleted photosystem II (PSII) membranes at room temperature. The ini...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00490a014

    authors: Buser CA,Thompson LK,Diner BA,Brudvig GW

    更新日期:1990-09-25 00:00:00

  • Evidence that the Rhodopsin Kinase (GRK1) N-Terminus and the Transducin Gα C-Terminus Interact with the Same "Hydrophobic Patch" on Rhodopsin TM5.

    abstract::Phosphorylation of G protein-coupled receptors (GPCRs) terminates their ability to couple with and activate G proteins by increasing their affinity for arrestins. Unfortunately, detailed information regarding how GPCRs interact with the kinases responsible for their phosphorylation is still limited. Here, we purified ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00328

    authors: Jones Brunette AM,Sinha A,David L,Farrens DL

    更新日期:2016-06-07 00:00:00

  • Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae.

    abstract::Two dioxygenases (ARD and ARD') were cloned from Klebsiella pneumoniae that catalyze different oxidative decomposition reactions of an advanced aci-reductone intermediate, CH(3)SCH(2)CH(2)COCH(OH)=CH(OH) (I), in the methionine salvage pathway. The two enzymes are remarkable in that they have the same polypeptide seque...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010110y

    authors: Dai Y,Pochapsky TC,Abeles RH

    更新日期:2001-05-29 00:00:00

  • Effects of DNA binding proteins on DNA methylation in vitro.

    abstract::The inheritance of DNA methylation patterns may play an important role in the stability of the differentiated state. We have therefore studied the inhibitory effects of DNA binding proteins on DNA methylation in vitro. Mouse L1210 cells grown in the presence of 5-azacytidine acquire hemimethylated sites in their DNA. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00326a021

    authors: Kautiainen TL,Jones PA

    更新日期:1985-02-26 00:00:00

  • Kinetic studies on the mechanism of pepsin action.

    abstract::The linear noncompetitive inhibition of the pepsin-catalyzed hydrolysis of Ac-Phe-Phe-Gly at pH 2.1 by L-Ac-Phe, L-Ac-Phe-NH2, and L-Ac-Phe-OEt has been claimed to substantiate the ordered release of products specified by the amino-enzyme mechanism for pepsin action. According to this interpretation, the binding of in...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00674a023

    authors: Silver MS,Stoddard M

    更新日期:1975-02-11 00:00:00

  • Double-strand break formation during nucleotide excision repair of a DNA interstrand cross-link.

    abstract::The DNA interstrand cross-link (ICL) resulting from the C4'-oxidized abasic site (C4-AP) is a unique clustered lesion comprised of a cross-link adjacent to a nick. The ICL is a substrate for the UvrABC nucleotide excision repair system. The strand containing the nick is preferentially incised, but the nick influences ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901006b

    authors: Sczepanski JT,Jacobs AC,Van Houten B,Greenberg MM

    更新日期:2009-08-18 00:00:00

  • Effects of pH and calcium ions on the conformational transitions in silk fibroin using 2D Raman correlation spectroscopy and 13C solid-state NMR.

    abstract::Silk fibroin exists in a number of different states, such as silk I and silk II, with different properties largely defined by differences in secondary structure composition. Numerous attempts have been made to control the transitions from silk I to silk II in vitro to produce high-performance materials. Of all the fac...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049344i

    authors: Zhou P,Xie X,Knight DP,Zong XH,Deng F,Yao WH

    更新日期:2004-09-07 00:00:00

  • Mode of Interaction of the Signal-Transducing Protein EIIA(Glc) with the Maltose ABC Transporter in the Process of Inducer Exclusion.

    abstract::Enzyme IIA(Glc) (EIIA(Glc)) of the phosphoenolpyruvate phosphotransferase system for the uptake of glucose in Escherichia coli and Salmonella inhibits the maltose ATP-binding cassette transporter (MalE-FGK2) by interaction with the nucleotide-binding and -hydrolyzing subunit MalK, a process termed inducer exclusion. W...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00721

    authors: Wuttge S,Licht A,Timachi MH,Bordignon E,Schneider E

    更新日期:2016-09-27 00:00:00

  • A new model to describe extrinsic protein binding to phospholipid membranes of varying composition: application to human coagulation proteins.

    abstract::We introduce here a new model to describe the binding of extrinsic membrane proteins to acidic lipid membranes. In this view, macroscopic binding affinity is determined by two processes: nonspecific adsorption of protein to the membrane surface and association of acidic lipids with specific sites on the bound protein....

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00444a045

    authors: Cutsforth GA,Whitaker RN,Hermans J,Lentz BR

    更新日期:1989-09-05 00:00:00

  • Basic proline-rich proteins from human parotid saliva: complete covalent structures of proteins IB-1 and IB-6.

    abstract::The complete amino acid sequences of two basic proline-rich proteins, IB-1 and IB-6, from human parotid saliva have been determined. Fragments for sequence analysis were obtained by enzymatic digestions. The proteins have molecular weights of 9571 (IB-1) and 11,530 (IB-6) and contain 34 and 39 mol % proline, respectiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00357a013

    authors: Kauffman D,Hofmann T,Bennick A,Keller P

    更新日期:1986-05-06 00:00:00

  • Proton and deuteron nuclear magnetic relaxation dispersion studies of Ca2+-Mn2+-lentil lectin and Ca2+-Mn2+-pea lectin: evidence for a site of solvent exchange in common with concanavalin A.

    abstract::Measurements of the magnetic field dependence of the longitudinal magnetic relaxation rates (NMRD profiles) of solvent protons and deuterons led to the discovery of two classes of solvent binding sites in Ca2+-Mn2+-concanavalin A (CMPL) [Koenig, S. H., Brown, R. D., III, & Brewer, C. F. (1985) Biochemistry (second of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00340a004

    authors: Bhattacharyya L,Brewer CF,Brown RD 3rd,Koenig SH

    更新日期:1985-09-10 00:00:00

  • Properties of interacting aspartic acid and lysine residues in the lactose permease of Escherichia coli.

    abstract::The side chains of the interacting pair Asp237(helix VII)-Lys358(helix XI) or Asp240(helix VII)-Lys319(helix X) in the lactose permease of Escherichia coli were extended by replacement with Glu and/or Arg or by site-specific derivatization of single-Cys replacement mutants. Iodoacetic acid was used to carboxymethylate...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00089a019

    authors: Sahin-Tóth M,Kaback HR

    更新日期:1993-09-28 00:00:00

  • Requirement of histidine 217 for ubiquinone reductase activity (Qi site) in the cytochrome bc1 complex.

    abstract::Folding models suggest that the highly conserved histidine 217 of the cytochrome b subunit from the cytochrome bc1 complex is close to the quinone reductase (Qi) site. This histidine (bH217) in the cytochrome b polypeptide of the photosynthetic bacterium Rhodobacter capsulatus has been replaced with three other residu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00169a014

    authors: Gray KA,Dutton PL,Daldal F

    更新日期:1994-01-25 00:00:00

  • Position-dependent local motions in spin-labeled analogues of a short alpha-helical peptide determined by electron spin resonance.

    abstract::We have used electron spin resonance and circular dichroism to examine and compare the dynamics in two analogues of the Ala-based 3K(I) peptide [Marqusee, S., Robbins, V.H., & Baldwin, R. L. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 5286-5290], labeled at positions 4 and 8, throughout the alpha-helix----coil transition...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00103a016

    authors: Miick SM,Todd AP,Millhauser GL

    更新日期:1991-10-01 00:00:00

  • Deuteron nuclear magnetic resonance studies of phase equilibria in a lecithin-water system.

    abstract::Water deuteron NMR spectra have been studied for the system dipalmitoyllecithin (DPL)-heavy water (D2O) at different compositions and temperatures. From an analysis of the spectra in terms of quadrupole splittings, a phase diagram has been constructed for the temperature range 25-60 degrees C and the composition range...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00645a014

    authors: Ulmius J,Wennerström H,Lindblom G,Arvidson G

    更新日期:1977-12-27 00:00:00

  • Thiophosphoryl guanine nucleotide analogues inhibit the (Na+,K+)-ATPase.

    abstract::The effects of several guanine nucleotide analogues on (Na+,K+)-ATPase activity of membranes isolated from several tissues were analyzed to determine if a G-protein might be involved in the hormonal regulation of the (Na+,K+)-ATPase. Submillimolar concentrations of GTP gamma S, but not GMPPNP, inhibit rat skeletal mus...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00241a014

    authors: McGill DL

    更新日期:1991-07-09 00:00:00

  • Structural insights into the membrane fusion mechanism mediated by influenza virus hemagglutinin.

    abstract::Membrane fusion is involved in many fundamental cellular processes and entry of enveloped viruses into host cells. Influenza type A virus HA has long served as a paradigm for mechanistic studies of protein-mediated membrane fusion via large-scale structural rearrangements induced by acidic pH. Here we report the newly...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi401525h

    authors: Ni F,Chen X,Shen J,Wang Q

    更新日期:2014-02-11 00:00:00

  • Tying up the Ends: Plasticity in the Recognition of Single-Stranded DNA at Telomeres.

    abstract::Telomeres terminate nearly exclusively in single-stranded DNA (ssDNA) overhangs comprised of the G-rich 3' end. This overhang varies widely in length from species to species, ranging from just a few bases to several hundred nucleotides. These overhangs are not merely a remnant of DNA replication but rather are the res...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00496

    authors: Lloyd NR,Dickey TH,Hom RA,Wuttke DS

    更新日期:2016-09-27 00:00:00

  • Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases.

    abstract::Adenylosuccinate synthetase catalyzes the first committed step in the de novo biosynthesis of AMP, coupling L-aspartate and IMP to form adenylosuccinate. Km values of IMP and 2'-deoxy-IMP are nearly identical with each substrate supporting comparable maximal velocities. Nonetheless, the Km value for L-aspartate and th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0607498

    authors: Iancu CV,Zhou Y,Borza T,Fromm HJ,Honzatko RB

    更新日期:2006-09-26 00:00:00

  • Hydrogen bonding networks tune proton-coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia.

    abstract::Multielectron multiproton reactions play an important role in both biological systems and chemical reactions involved in energy storage and manipulation. A key strategy employed by nature in achieving such complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500854p

    authors: Judd ET,Stein N,Pacheco AA,Elliott SJ

    更新日期:2014-09-09 00:00:00

  • Characterization of recombinant Saccharomyces cerevisiae manganese-containing superoxide dismutase and its H30A and K170R mutants expressed in Escherichia coli.

    abstract::All known Mn-containing superoxide dismutases (MnSODs) have a highly conserved histidine (His-30 in Escherichia coli FeSOD) in the active-site channel, and nearly all have an active-site arginine (Arg-170) that has been proposed to play a combined structural and functional role [Chan et al., Arch. Biochem. Biophys. 27...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980167t

    authors: Borders CL Jr,Bjerrum MJ,Schirmer MA,Oliver SG

    更新日期:1998-08-11 00:00:00

  • Regulation of the concentration of pre beta high-density lipoprotein in normal plasma by cell membranes and lecithin-cholesterol acyltransferase activity.

    abstract::A minor fraction of plasma high-density lipoprotein (pre beta-1 HDL) has been shown to promote cholesterol efflux from peripheral cell membranes [Castro, G. R., & Fielding, C. J. (1988) Biochemistry 27, 25-29]. When isolated native plasma is incubated at 37 degrees C, this fraction is specifically decreased. On the ot...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00160a022

    authors: Miida T,Kawano M,Fielding CJ,Fielding PE

    更新日期:1992-11-17 00:00:00

  • The Heliothis virescens cadherin protein expressed in Drosophila S2 cells functions as a receptor for Bacillus thuringiensis Cry1A but not Cry1Fa toxins.

    abstract::Genetic knockout of the BtR4 gene encoding the Heliothis virescens cadherin-like protein (HevCaLP) is linked to resistance against Cry1Ac toxin from Bacillus thuringiensis. However, the functional Cry1Ac receptor role of this protein has not been established. We previously proposed HevCaLP as a shared binding site for...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0606703

    authors: Jurat-Fuentes JL,Adang MJ

    更新日期:2006-08-15 00:00:00

  • RuvB protein-mediated ATP hydrolysis: functional asymmetry in the RuvB hexamer.

    abstract::A survey of RuvB protein-mediated ATP hydrolysis yields the following observations. (1) The RuvB protein exhibits a DNA-independent ATPase activity with a turnover number (based on a RuvB monomer) approaching 6 min-1 and a Km of 154 microM. Single-stranded DNA and linear duplex DNA have small but significant effects o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00030a019

    authors: Marrione PE,Cox MM

    更新日期:1995-08-01 00:00:00

  • Proton NMR and structural features of a 24-nucleotide RNA hairpin.

    abstract::The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing requirements for coat protein binding known from bioche...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00019a030

    authors: Borer PN,Lin Y,Wang S,Roggenbuck MW,Gott JM,Uhlenbeck OC,Pelczer I

    更新日期:1995-05-16 00:00:00