Abstract：
:Induced fit has been postulated to be an important component of ligand interactions with proteins, including protein-DNA interactions. We imagined that the entropic cost of induced fit might be highly dependent on the local protein sequence context around critical contact residues. To investigate this question, we analyzed the basis for active or inactive phenotypes found in a library of combinatorial sequence variants of a surface-located helix-loop peptide which is essential for the anticodon-binding activity of a class I tRNA synthetase. Molecular dynamics simulations of the domain encompassing the helix-loop peptide of the active variants consistently demonstrated fixation of the local motion of five critical (for function) residues which are highly mobile in inactive variants. Additional experiments with other rationally chosen mutants extended the correlation between phenotype and motion of these vital residues. We propose that the need for fixation of local motion is an important constraint on sequences of surface peptides which form parts of RNA-binding sites. The fixation of motion of critical residues in the unbound protein can significantly reduce the entropic cost of complex formation by induced fit.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Ribas de Pouplana L,Auld DS,Kim S,Schimmel Pdoi
10.1021/bi960256asubject
Has Abstractpub_date
1996-06-25 00:00:00pages
8095-102issue
25eissn
0006-2960issn
1520-4995pii
bi960256ajournal_volume
35pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:S100A1, a member of the S100 protein family, is an EF-hand containing Ca(2+)-binding protein (93 residues per subunit) with noncovalent interactions at its dimer interface. Each subunit of S100A1 has four alpha-helices and a small antiparallel beta-sheet consistent with two helix-loop-helix calcium-binding domains [Ba...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0118308
更新日期：2002-01-22 00:00:00
abstract：:We have used thrombin to cleave apolipoprotein C-III-1 into two fragments constituting residues 1-40 (apoLP-C-III-A) and 41-79 (apoLP-C-III-B). The lipid binding properties of these fragments with dimyristoyl- and 1-palmitoyl-2-oleoylphosphatidylcholines have been determined using circular dichroic and intrinsic trypt...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00644a004
更新日期：1977-12-13 00:00:00
abstract：:The initial step of infection of blood cells with the human immunodeficiency virus, HIV, is the formation of a complex of the viral envelope protein gp120 and its human receptor CD4. We have examined structural features of recombinant soluble CD4 (sCD4) by chemical modification of arginine residues with hydroxyphenylg...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi011626k
更新日期：2002-02-12 00:00:00
abstract：:Zinc finger nucleases (ZFNs) have been used to direct precise modifications of the genetic information in living cells at high efficiency. An important consideration in the design of ZFNs is the number of zinc fingers that are required for efficient and specific cleavage. We examined dimeric ZFNs composed of [1]+[1], ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200393g
更新日期：2011-06-07 00:00:00
abstract：:The genomic hypervariation of human immunodeficiency virus 1 (HIV-1) could result from misincorporations by the viral reverse transcriptase. We developed an assay for reverse transcriptase fidelity during RNA-dependent as well as DNA-dependent DNA polymerization in vitro. A lacZ alpha RNA fragment transcribed by T3 RN...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00119a002
更新日期：1992-02-04 00:00:00
abstract：:From an evolutionary point of view, plant and animal ferritins arose from a common ancestor, but plant ferritin exhibits different features as compared with the animal analogue. One major difference is that the 4-fold channels naturally occurring in plant ferritin are hydrophilic, whereas the 4-fold channels in animal...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi500066m
更新日期：2014-04-15 00:00:00
abstract：:MutY protein, a DNA glycosylase found in Escherichia coli, recognizes dA:dG, dA:8-oxodG, and dA:dC mismatches in duplex DNA, excising the adenine moiety. We have investigated the mechanism of action of MutY, addressing several points of disagreement raised by previous studies of this enzyme. MutY forms a covalent inte...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi981066y
更新日期：1998-09-08 00:00:00
abstract：:Amyloid fibrils have been classically defined as linear, nonbranched polymeric proteins with a cross beta-sheet structure and the ability to alter the optical properties of the amyloid-specific dye Congo Red. Mounting evidence suggests that soluble oligomeric peptide assemblies approximately 2-20 nm in diameter are cr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi700247y
更新日期：2007-06-19 00:00:00
abstract：:The effects of phosphorylation at Ser40 of rat tyrosine hydroxylase on the affinities of catechols have been determined with both the ferric and ferrous forms of the enzyme. Phosphorylation had no effect on the Ki value for the inhibition of the ferrous enzyme by either dopamine or DOPA when the initial rate of turnov...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi980582l
更新日期：1998-06-23 00:00:00
abstract：:The flavoenzyme tryptophan 2-monooxygenase catalyzes the oxidation of tryptophan to indoleacetamide, carbon dioxide, and water. The enzyme is a homologue of l-amino acid oxidase. In the structure of l-amino acid oxidase complexed with aminobenzoate, Tyr372 hydrogen bonds with the carboxylate of the inhibitor in the ac...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi035300i
更新日期：2003-12-02 00:00:00
abstract：:The structure and backbone dynamics of an extended second transmembrane segment (TM2e) of the human neuronal glycine receptor alpha(1) subunit in sodium dodecyl sulfate micelles were studied by (1)H and (15)N solution-state NMR. The 28-amino acid segment contained the consensus TM2 domain plus part of the linker betwe...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi026767g
更新日期：2003-04-08 00:00:00
abstract：:To address the targeting of G protein-coupled receptors to caveolae-related lipid rafts (CLR), we studied the human B2 (B2R) and B1 (B1R) bradykinin receptor subtypes in HEK293 cells. CLR were enriched on the basis of their unique buoyant density and composition of cholesterol, caveolin-1, and flotillin-1 but not clat...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi020231d
更新日期：2002-12-03 00:00:00
abstract：:Upon injury of a blood vessel, activated factor VII (FVIIa) forms a high-affinity complex with its allosteric regulator, tissue factor (TF), and initiates blood clotting. Active site-inhibited factor VIIa (FVIIai) binds to TF with even higher affinity. We compared the interactions of FVIIai and FVIIa with soluble TF (...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi010283n
更新日期：2001-08-07 00:00:00
abstract：:Transporters from the SLC13 family couple the transport of two to four Na+ ions with a di- or tricarboxylate, such as succinate or citrate. We have previously modeled mammalian members of the SLC13 family, including the Na+/dicarboxylate cotransporter NaDC1 (SLC13A2), based on a structure of the bacterial homologue Vc...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.7b00503
更新日期：2017-08-22 00:00:00
abstract：:The organization of the higher order structure of chromatin has been examined in chicken erythrocyte. Chromatin solubilized during the time course of a gentle micrococcal nuclease digestion of nuclei shows a continuous variation in the distribution of molecular weights. Electron microscopy studies of large chromatin f...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00553a002
更新日期：1980-06-10 00:00:00
abstract：:The solution structures of peptide antigens from the receptor binding domains of Pseudomonas aeruginosa strains PAO and KB7 have been determined using two-dimensional 1H NMR techniques. Ensembles of solution conformations for the trans forms of these 17-residue disulfide-bridged peptides have been generated using a si...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00050a005
更新日期：1995-12-19 00:00:00
abstract：:The secondary structure of protein kinase C alpha (PKC alpha) has been studied using infrared spectroscopy in the presence of both H(2)O and D(2)O buffers. In the absence of ligands at 20 degrees C, it was shown that beta-sheet is the major component, representing about 44% of the total structure, whereas the alpha-he...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi035128i
更新日期：2004-03-02 00:00:00
abstract：:Competitive inhibition of the monophenolase reaction of tyrosinase by a variety of compounds was investigated with respect to temperature and pH. Derivatives of benzoic acid as well as p-nitrophenol were the best inhibitors. Toluene and several N-heterocycles were all weak inhibitors. Thermodynamic parameters of tolue...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00185a010
更新日期：1994-05-17 00:00:00
abstract：:The kinetics of the phospholipase A2-catalyzed hydrolysis of bilayer vesicles and mixed micelles of several oxyglycero and thioglycero analogues of phospholipids have been studied. The results with vesicles show that, depending on the source of the enzyme, the rates of hydrolysis of the oxy-containing long-chain phosp...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00149a014
更新日期：1992-09-01 00:00:00
abstract：:Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP- and glutamine-dependent formation of formylglycinamidine ribonucleotide, ADP, P(i), and glutamate in the fourth step of de novo purine biosynthesis. Like all amidotransferases (ATs), FGAR-AT is proposed to channel ammonia between a glutamin...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi049127h
更新日期：2004-08-17 00:00:00
abstract：:Chemoenzymatic glycan remodeling by endoglycosidase-catalyzed deglycosylation and reglycosylation is emerging as an attractive approach for producing homogeneous glycoforms of antibodies, and the success of this approach depends on the discovery of efficient endoglycosidases and their glycosynthase mutants. We report ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00719
更新日期：2018-09-04 00:00:00
abstract：:The structural domains of human apolipoprotein(a) [apo(a)] and its interaction with apolipoprotein B-100 (apo B-100) in the lipoprotein(a) [Lp(a)] particle were investigated by limited proteolysis with thermolysin and cathepsin D. We characterized the proteolytic products by sodium dodecyl sulfate-polyacrylamide gradi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00177a026
更新日期：1994-03-22 00:00:00
abstract：:Carboxyl ester lipase (CEL; EC 3.1.1.13) hydrolyzes cholesteryl esters and retinyl esters in vitro. In vivo, pancreatic CEL is thought to liberate cholesterol and retinol from their esters prior to absorption in the intestine. CEL is also a major lipase in the breast milk of many mammals, including humans and mice, an...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi981679a
更新日期：1999-03-30 00:00:00
abstract：:One of the key pathological features of Alzheimer's disease is the aggregation of tau protein. We are therefore searching for compounds capable of inhibiting this reaction. On the basis of an initial screen of 200000 compounds [Pickhardt, M., Gazova, Z., von Bergen, M., Khlistunova, I., Wang, Y., Hascher, A., Mandelko...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi700878g
更新日期：2007-09-04 00:00:00
abstract：:An important subject for elucidating membrane protein (MP) folding is how transmembrane helices (TMHs) insert into and dissociate from membranes. We investigated helix dissociation kinetics and insertion topology by means of intervesicular transfer of the fluorophore-labeled completely hydrophobic model transmembrane ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi026191v
更新日期：2002-10-15 00:00:00
abstract：:The chemoreceptors of Escherichia coli are homodimeric membrane proteins that cluster in patches near the cell poles. They convert environmental stimuli into intracellular signals that control flagellar rotation. The functional domains of a receptor are physically separated by the cell membrane. Chemoeffectors bind to...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048969d
更新日期：2005-02-01 00:00:00
abstract：:A steady-state kinetic analysis was conducted of the overall aminoacylation reaction catalyzed by isoleucyl-tRNA synthetase. The patterns of Lineweaver-Burk plots obtained indicated that tRNA adds to the enzyme only after isoleucyl adenylate formation and pyrophosphate release. These kinetic patterns were consistent w...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00580a018
更新日期：1979-06-26 00:00:00
abstract：:Bacteriocins are bacterial peptides with specific activity against competing species. They hold great potential as natural preservatives and for their probiotic effects. We show here nuclear magnetic resonance-based evidence that glycocin F, a 43-amino acid bacteriocin from Lactobacillus plantarum, contains two β-link...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200217u
更新日期：2011-04-12 00:00:00
abstract：:We have investigated the effects of mixed Na+: Mg2+ ionic solutions on the stability of the nonspecific lac repressor-DNA complex. The effects of Mg2+ are simply interpreted in terms of its role as a competitor (with repressor) for DNA sites. From these studies, the binding constant of the Mg-DNA complex can be determ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00641a005
更新日期：1977-11-01 00:00:00
abstract：:Carbamoylation and reductive methylation of tubulin have been shown previously to inhibit microtubule assembly, probably by attack on essential internal lysine residues [Mellado, W., Slebe, J., & Maccioni, R.B. (1982) Biochem. J. 203, 675-681; Szasz, J., Burns, R., & Sternlicht, H. (1982) J. Biol. Chem. 257, 3697-3704...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00403a027
更新日期：1988-02-09 00:00:00
