当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance.

Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance.

Abstract：

:Crowding, which characterizes the interior of all living cells, has been shown to dramatically affect biochemical processes, leading to stabilization of compact morphologies, enhanced macromolecular associations, and altered reaction rates. Due to the crowding-mediated shift in binding equilibria toward association, crowding agents were proposed to act as a metabolic buffer, significantly extending the range of intracellular conditions under which interactions occur. Crowding may, however, impose a liability because, by greatly and generally enhancing macromolecular association, it can lead to irreversible interactions. To better understand the physical determinants and physiological consequences of crowding-mediated buffering, we studied the effects of crowding, or excluded volume, on DNA structures. Results obtained from isothermal titration calorimetry (ITC) and UV melting experiments indicate that crowding-induced effects are marginal under conditions that a priori favor association of DNA strands but become progressively larger when conditions deteriorate. As such, crowding exerts "genuine" buffering activity. Unexpectedly, crowding-mediated effects are found to include enthalpy terms that favorably contribute to association processes. We propose that these enthalpy terms and preferential stabilization derive from a reconfiguration of DNA hydration that occurs in dense DNA-rich phases obtained in crowded environments.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Goobes R,Kahana N,Cohen O,Minsky A

doi

10.1021/bi026775x

subject

Has Abstract

pub_date

2003-03-04 00:00:00

pages

2431-40

issue

8

eissn

0006-2960

issn

1520-4995

journal_volume

42

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Glyoxylate carboligase: a unique thiamin diphosphate-dependent enzyme that can cycle between the 4'-aminopyrimidinium and 1',4'-iminopyrimidine tautomeric forms in the absence of the conserved glutamate.

    abstract：:Glyoxylate carboligase (GCL) is a thiamin diphosphate (ThDP)-dependent enzyme, which catalyzes the decarboxylation of glyoxylate and ligation to a second molecule of glyoxylate to form tartronate semialdehyde (TSA). This enzyme is unique among ThDP enzymes in that it lacks a conserved glutamate near the N1' atom of Th...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi300893v

    authors： Nemeria N,Binshtein E,Patel H,Balakrishnan A,Vered I,Shaanan B,Barak Z,Chipman D,Jordan F

    更新日期：2012-10-09 00:00:00

  • A circumventing role for the non-native intermediate in the folding of β-lactoglobulin.

    abstract：:Folding experiments have suggested that some proteins have kinetic intermediates with a non-native structure. A simple G ̅o model does not explain such non-native intermediates. Therefore, the folding energy landscape of proteins with non-native intermediates should have characteristic properties. To identify such pro...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi200241a

    authors： Sakurai K,Fujioka S,Konuma T,Yagi M,Goto Y

    更新日期：2011-07-26 00:00:00

  • Volume changes during enzyme reactions: indications of enzyme pulsation during fumarase catalysis.

    abstract：:Overall activation volumes for multistep reactions are not usually pressure independent. The present investigation gives a quantitative description of this effect under Theory. Simple relations are obtained which can easily be applied to experimental data and which allow more insight into the dynamics of enzyme reacti...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00405a024

    authors： Butz P,Greulich KO,Ludwig H

    更新日期：1988-03-08 00:00:00

  • Kinetic and Spectroscopic Characterization of the Catalytic Ternary Complex of Tryptophan 2,3-Dioxygenase.

    abstract：:The first step of the kynurenine pathway for l-tryptophan (l-Trp) degradation is catalyzed by heme-dependent dioxygenases, tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase. In this work, we employed stopped-flow optical absorption spectroscopy to study the kinetic behavior of the Michaelis complex of C...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.0c00179

    authors： Geng J,Weitz AC,Dornevil K,Hendrich MP,Liu A

    更新日期：2020-08-04 00:00:00

  • Identification of Asp-130 as the catalytic nucleophile in the main alpha-galactosidase from Phanerochaete chrysosporium, a family 27 glycosyl hydrolase.

    abstract：:Characterization of the complete gene sequence encoding the alpha-galactosidase from Phanerochaete chrysosporium confirms that this enzyme is a member of glycosyl hydrolase family 27 [Henrissat, B., and Bairoch, A. (1996) Biochem. J. 316, 695-696]. This family, together with the family 36 alpha-galactosidases, forms g...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0008074

    authors： Hart DO,He S,Chany CJ 2nd,Withers SG,Sims PF,Sinnott ML,Brumer H 3rd

    更新日期：2000-08-15 00:00:00

  • NMR structure determination of a novel conotoxin, [Pro 7,13] alpha A-conotoxin PIVA.

    abstract：:A high-resolution solution conformation of a novel conotoxin, [Pro 7,13] alpha A-conotoxin PIVA, GCCGSYPNAACHPCSCKDROSYCGQ-NH2, has been determined by two-dimensional 1H NMR methods and distance geometry calculations. The total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi962301k

    authors： Han KH,Hwang KJ,Kim SM,Kim SK,Gray WR,Olivera BM,Rivier J,Shon KJ

    更新日期：1997-02-18 00:00:00

  • Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy.

    abstract：:The dynamics of individual DNA molecules undergoing orthogonal field alternating gel electrophoresis (OFAGE) have been studied by use of T2 DNA molecules labeled with a dye and visualized with a fluorescence microscope. The mechanism of reorientation used by a molecule to align itself in the direction of the new ortho...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00465a036

    authors： Gurrieri S,Rizzarelli E,Beach D,Bustamante C

    更新日期：1990-04-03 00:00:00

  • Detergents stabilize the conformation of phosphodiesterase 6.

    abstract：:Membrane-bound phosphodiesterase 6 (PDE6) plays an important role in visual signal transduction by regulating cGMP levels in rod photoreceptor cells. Our understanding of PDE6 catalysis and structure suffers from inadequate characterization of the α and β subunit catalytic core, interactions of the core with two intri...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi2014695

    authors： Baker BY,Palczewski K

    更新日期：2011-11-08 00:00:00

  • Structure and vectorial properties of proteoliposomes containing cytochrome oxidase in the submitochondrial orientation.

    abstract：:Cytochrome oxidase proteoliposomes were prepared from bovine heart oxidase. Size distributions determined by quasi-elastic light scattering (QELS) showed that there was a small population of large vesicles (120-200-nm diameter) and a large population of small vesicles (50-100-nm diameter). Trapping cytochrome c inside...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00468a010

    authors： Cooper CE,Nicholls P

    更新日期：1990-04-24 00:00:00

  • Mechanistic studies of the methyltransferase from Clostridium thermoaceticum: origin of the pH dependence of the methyl group transfer from methyltetrahydrofolate to the corrinoid/iron-sulfur protein.

    abstract：:A methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase (MeTr) from Clostridium thermoaceticum catalyzes the transfer of the N5 methyl group from (6S)-methyltetrahydrofolate (CH3-H4folate) to the cobalt center of a corrinoid/iron-sulfur protein (C/Fe-SP). The methylcobamide product is the first in a s...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00046a013

    authors： Zhao S,Roberts DL,Ragsdale SW

    更新日期：1995-11-21 00:00:00

  • Binding of bleomycin to DNA: intercalation of the bithiazole rings.

    abstract：:At pH 5.5, binding of bleomycin relaxed supercoiled ColE1 DNA without breaking it. Binding of tripeptide S, a fragment of the drug containing the bithiazole rings, also relaxed and then recoiled supercoiled DNA, at pH 5.5 and at pH 8.0, where bleomycin is normally active. The unwinding angle was 12 degrees. Both compo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00568a015

    authors： Povirk LF,Hogan M,Dattagupta N

    更新日期：1979-01-09 00:00:00

  • Structure, spectroscopic, and redox properties of Rhodobacter sphaeroides reaction centers bearing point mutations near the primary electron donor.

    abstract：:Single mutations of three amino acid residues in the vicinity of the primary electron donor, P, in the reaction center (RC) from Rhodobacter (Rb.) sphaeroides were constructed and characterized in order to study the effects of hydrogen-bonding on the physical properties of P. The mutations, Phe M197-->Tyr, Met L248-->...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00210a041

    authors： Wachtveitl J,Farchaus JW,Das R,Lutz M,Robert B,Mattioli TA

    更新日期：1993-11-30 00:00:00

  • Purification and properties of acyl coenzyme A thioesterase II from Rhodopseudomonas sphaeroides.

    abstract：:A high molecular weight acyl coenzyme A (acyl-CoA) thioesterase, designated thioesterase II, has been purified 5300-fold from photoheterotrophically grown cells of Rhodopseudomonas sphaeroides. In contrast to R. sphaeroides acyl-CoA thioesterase I [Boyce, S.G., & Lueking, D.R. (1984) Biochemistry 23, 141-147], thioest...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00357a029

    authors： Seay T,Lueking DR

    更新日期：1986-05-06 00:00:00

  • Peptoid-Substituted Hybrid Antimicrobial Peptide Derived from Papiliocin and Magainin 2 with Enhanced Bacterial Selectivity and Anti-inflammatory Activity.

    abstract：:Antimicrobial peptides (AMPs) are important components of the host innate immune system. Papiliocin is a 37-residue AMP purified from larvae of the swallowtail butterfly Papilio xuthus. Magainin 2 is a 23-residue AMP purified from the skin of the African clawed frog Xenopus laevis. We designed an 18-residue hybrid pep...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00392

    authors： Shin A,Lee E,Jeon D,Park YG,Bang JK,Park YS,Shin SY,Kim Y

    更新日期：2015-06-30 00:00:00

  • Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.

    abstract：:The bacterial phosphotriesterase (PTE) from Pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters at rates close to the diffusion limit. X-ray diffraction studies have shown that a binuclear metal center is positioned in the active site of PTE and that this complex is responsible for the activation o...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi800971v

    authors： Kim J,Tsai PC,Chen SL,Himo F,Almo SC,Raushel FM

    更新日期：2008-09-09 00:00:00

  • Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR.

    abstract：:The structure of the 56-residue B1 immunoglobulin-binding domain from streptococcal protein G has been determined in two different crystal forms. The crystal structures were deduced by molecular replacement, based on the structure of the B2 domain (Brookhaven accession code 1PGX). Final R values are 0.174 and 0.198 fo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：

    authors： Gallagher T,Alexander P,Bryan P,Gilliland GL

    更新日期：1994-04-19 00:00:00

  • Evaluation of membrane phase behavior as a tool to detect extrinsic protein-induced domain formation: binding of prothrombin to phosphatidylserine/phosphatidylcholine vesicles.

    abstract：:The temperature-composition phase diagram of mixed dimyristoylphosphatidylserine (DMPS) and dimyristoylphosphatidylcholine (DMPC) small unilamellar vesicles was determined in the presence and absence of bound bovine prothrombin by monitoring the phospholipid order-disorder phase separation using diphenylhexatriene (DP...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00480a023

    authors： Tendian SW,Lentz BR

    更新日期：1990-07-17 00:00:00

  • Characterization of cDNA clones encoding rabbit and human serum paraoxonase: the mature protein retains its signal sequence.

    abstract：:Serum paraoxonase hydrolyzes the toxic metabolites of a variety of organophosphorus insecticides. High serum paraoxonase levels appear to protect against the neurotoxic effects of organophosphorus substrates of this enzyme [Costa et al. (1990) Toxicol. Appl. Pharmacol. 103, 66-76]. The amino acid sequence accounting f...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00106a010

    authors： Hassett C,Richter RJ,Humbert R,Chapline C,Crabb JW,Omiecinski CJ,Furlong CE

    更新日期：1991-10-22 00:00:00

  • Substrate binding to chloramphenicol acetyltransferase: evidence for negative cooperativity from equilibrium and kinetic constants for binary and ternary complexes.

    abstract：:Chloramphenicol acetyltransferase (CAT) catalyzes the acetyl-CoA-dependent acetylation of chloramphenicol by a ternary complex mechanism with a rapid equilibrium and essentially random order of addition of substrates. Such a kinetic mechanism for a two-substrate reaction provides an opportunity to compare the affinity...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00108a029

    authors： Ellis J,Bagshaw CR,Shaw WV

    更新日期：1991-11-05 00:00:00

  • Molecular homogeneity of the histone content of HeLa chromatin subunits.

    abstract：:Interaction of affinity chromatographically purified antihistone H3 and antihistone H4 with isolated HeLa core particles, followed by separation of unreacted and reacted particles by sedimentation, demonstrates that every core particle contains these histones. Taken together with our previous data indicating the prese...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00643a033

    authors： Bustin M,Simpson RT,Sperling R,Goldblatt D

    更新日期：1977-11-29 00:00:00

  • Functional epitopes for site 1 of human prolactin.

    abstract：:Human prolactin (hPRL) binds two human prolactin receptor molecules, creating active heterotrimeric complexes. Receptors bind dissimilar hormone surfaces termed site 1 and site 2 in an obligate ordered process. We sought to map the functional epitopes in site 1 of hPRL. Extensive alanine mutagenesis (102 of the 199 re...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi101838s

    authors： Rao GV,Brooks CL

    更新日期：2011-03-01 00:00:00

  • Kinetic stability may determine the interaction dynamics of the bifunctional protein DCoH1, the dimerization cofactor of the transcription factor HNF-1α .

    abstract：:The two disparate functions of DCoH1 (dimerization cofactor of HNF-1)/PCD (pterin-4a-carbinolamine dehydratase) are associated with a change in oligomeric state. DCoH dimers enhance the activity of the diabetes-associated transcription factor HNF-1α (hepatocyte nuclear factor-1α), while the PCD activity of DCoH1 homot...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi1015056

    authors： Rho H,Jones CN,Rose RB

    更新日期：2010-11-30 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

  • Structure of influenza virus neuraminidase B/Lee/40 complexed with sialic acid and a dehydro analog at 1.8-A resolution: implications for the catalytic mechanism.

    abstract：:Neuraminidase is one of the two glycoprotein spikes protruding from the influenza virus membrane. We have determined by X-ray crystallography the native structure of B/Lee/40 neuraminidase (NA) and the structures of its crystals soaked with a substrate, N-acetylneuraminyllactose (NANL), and an inhibitor, 2-deoxy-2,3-d...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00193a002

    authors： Janakiraman MN,White CL,Laver WG,Air GM,Luo M

    更新日期：1994-07-12 00:00:00

  • The active site structure of Thalassiosira weissflogii carbonic anhydrase 1.

    abstract：:X-ray absorption spectroscopy at the Zn K-edge indicates that the active site of the marine diatom Thalassiosira weissflogii carbonic anhydrase is strikingly similar to that of mammalian alpha-carbonic anhydrase enzymes. The zinc has three histidine ligands and a single water at 1.98 A. This is quite different from th...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi001416s

    authors： Cox EH,McLendon GL,Morel FM,Lane TW,Prince RC,Pickering IJ,George GN

    更新日期：2000-10-10 00:00:00

  • Structures of phage-display peptides that bind to the malarial surface protein, apical membrane antigen 1, and block erythrocyte invasion.

    abstract：:Apical membrane antigen 1 (AMA1) of the human malaria parasite Plasmodium falciparum is synthesized by schizont stage parasites and has been implicated in merozoite invasion of host erythrocytes. Phage-display techniques have recently been used to identify two 15-residue peptides, F1 and F2, which bind specifically to...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi034376b

    authors： Keizer DW,Miles LA,Li F,Nair M,Anders RF,Coley AM,Foley M,Norton RS

    更新日期：2003-08-26 00:00:00

  • Mapping of DNA alkylation sites induced by adozelesin and bizelesin in human cells by ligation-mediated polymerase chain reaction.

    abstract：:In this study, we have mapped the intracellular alkylation sites of adozelesin and bizelesin, two potent analogs of CC-1065, in individual genes at the single-nucleotide level. Human colon carcinoma cells were treated with adozelesin and bizelesin, and the position of adducts were mapped within the PGK-1 and p53 genes...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00185a043

    authors： Lee CS,Pfeifer GP,Gibson NW

    更新日期：1994-05-17 00:00:00

  • Campylobacter jejuni KDO8P Synthase, Its Inhibition by KDO8P Oxime, and Control of the Residence Time of Slow-Binding Inhibition.

    abstract：:3-Deoxy-d- manno-2-octulosonate-8-phosphate (KDO8P) synthase catalyzes the first step of lipopolysaccharide biosynthesis, namely condensation of phosphoenolpyruvate (PEP) with arabinose 5-phosphate (A5P), to produce KDO8P. We have characterized Campylobacter jejuni KDO8P synthase and its inhibition by KDO8P oxime. It ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.8b00748

    authors： Gama SR,Balachandran N,Berti PJ

    更新日期：2018-09-11 00:00:00

  • Interaction of a paramagnetic analogue of oxaloacetate with citrate synthase.

    abstract：:Electron paramagnetic resonance studies have indicated that nitrosodisulfonate binds to pig heart citrate synthase. Titration of the enzyme with nitrosodisulfonate revealed several binding sites for the probe per subunit with one site (KD approximately 0.1 mM) having a greater affinity than the others. The substrate, ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00584a028

    authors： Weidman SW,Drysdale GR

    更新日期：1979-08-21 00:00:00

  • Analysis of folding and unfolding reactions of cytochrome b5.

    abstract：:The guanidine hydrochloride- (GuHCl-) induced unfolding and refolding of a recombinant domain of bovine microsomal cytochrome b(5) containing the first 104 amino acid residues has been characterized by both transient and equilibrium spectrophotometric methods. The soluble domain is reversibly unfolded and the equilibr...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi991413j

    authors： Manyusa S,Mortuza G,Whitford D

    更新日期：1999-10-26 00:00:00