Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale.

Abstract:

:With knowledge of individual transfer free energies of chemical groups that become newly exposed on protein denaturation and assuming the group transfer free energy contributions are additive, it should be possible to predict the stability of a protein in the presence of denaturant. Unfortunately, several unresolved issues have seriously hampered quantitative development of this transfer model for protein folding/unfolding. These issues include the lack of adequate demonstration that group transfer free energies (DeltaG(tr)) are additive and independent of the choice of model compound, the problem arising from dependence of DeltaG(tr) on concentration scales, the lack of knowledge of activity coefficients, and the validity of the mathematical constructs used in obtaining DeltaG(tr) values. Regarding transfer from water to 1 M concentrations of the naturally occurring osmolytes, trimethylamine-N-oxide (TMAO), sarcosine, betaine, proline, glycerol, sorbitol, sucrose, trehalose, and urea, using cyclic glycylglycine, zwitterionic glycine peptides, and N-acetylglycine amide peptides as models for the peptide backbone of proteins, we set out to address these issues and obtain DeltaG(tr) values for the peptide backbone unit. We demonstrate experimental approaches that obviate the choice of concentration scale and demonstrate additivity in DeltaG(tr) of the peptide backbone unit for all solvent systems studied. Evidence is presented to show that the DeltaG(tr) values are independent of the chemical model studied, and experimental conditions are given to illustrate when the mathematical constructs are valid and when activity coefficients can be ignored. Resolution of the long-standing issues that have stymied development of the transfer model now make it possible to design transfer experiments that yield reliable and quantitative values for the interactions between osmolyte-containing solvents and native and unfolded protein.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Auton M,Bolen DW

doi

10.1021/bi035908r

subject

Has Abstract

pub_date

2004-02-10 00:00:00

pages

1329-42

issue

5

eissn

0006-2960

issn

1520-4995

journal_volume

43

pub_type

杂志文章
  • Inhibition mechanism of rat α₃β₄ nicotinic acetylcholine receptor by the Alzheimer therapeutic tacrine.

    abstract::Nicotinic acetylcholine receptors (nAChRs) were studied in detail in the past regarding their interaction with therapeutic and drug addiction related compounds. Using fast kinetic whole-cell recording, we have now studied effects of tacrine, an agent used clinically to treat Alzheimer's disease, on currents elicited b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101789y

    authors: Cheffer A,Ulrich H

    更新日期:2011-03-22 00:00:00

  • Crystal structures of thrombin complexed to a novel series of synthetic inhibitors containing a 5,5-trans-lactone template.

    abstract::The binding modes of four active site-directed, acylating inhibitors of human alpha-thrombin have been determined using X-ray crystallography. These inhibitors (GR157368, GR166081, GR167088, and GR179849) are representatives of a series utilizing a novel 5, 5-trans-lactone template to specifically acylate Ser195 of th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9830359

    authors: Jhoti H,Cleasby A,Reid S,Thomas PJ,Weir M,Wonacott A

    更新日期:1999-06-22 00:00:00

  • XAS investigation of the structure and function of Ni in acireductone dioxygenase.

    abstract::Acireductone dioxygenases (ARDs) are enzymes involved in the methionine recycle pathway, which regulates aspects of the cell cycle. Klebsiella pneumoniae produces two enzymes that share a common polypeptide sequence and differ only in the metal ion present. Reaction of acireductone (1,2-dihydroxy-3-keto-5-methylthiope...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi012209a

    authors: Al-Mjeni F,Ju T,Pochapsky TC,Maroney MJ

    更新日期:2002-05-28 00:00:00

  • Thiophilic adsorption: a comparison of model protein behavior.

    abstract::A newly recognized type of protein-ligand interaction phenomenon has resulted in the preparation of simple, nonionic, and highly specific gel derivatives for selective adsorption chromatography. The essential structure of the immobilized ligand can be represented as agarose-CH2CH2SO2CH2CH2SCH2CH2OH, which was prepared...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00396a049

    authors: Hutchens TW,Porath J

    更新日期:1987-11-03 00:00:00

  • Differences in secondary structure between packaged and unpackaged single-stranded DNA of bacteriophage phi X174 determined by Raman spectroscopy: a model for phi X174 DNA packaging.

    abstract::The single-stranded packaged genome (ssDNA) of bacteriophage phi X174 is shown by Raman spectroscopy to lack both the ordered phosphodiester backbone and base stacking, which are demonstrated for unpackaged, protein-free ssDNA. In solutions of moderate ionic strength, unpackaged ssDNA contains 36 +/- 7% of deoxyribosy...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00234a004

    authors: Benevides JM,Stow PL,Ilag LL,Incardona NL,Thomas GJ Jr

    更新日期:1991-05-21 00:00:00

  • Equilibrium binding of myristoyllysophosphatidylcholine to bovine myelin basic protein: an example of ligand-mediated acceptor association.

    abstract::The interaction of myristoyllysophosphatidylcholine with bovine myelin basic protein at pH 7.4 and 4.5, I = 0.48, has been investigated by a recycling partition equilibrium technique with Bio-Gel P-2 as the gel phase. Important points to emerge from this direct binding study are that it is a monomeric (not micellar) a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00378a002

    authors: Gow A,Winzor DJ,Smith R

    更新日期:1987-02-24 00:00:00

  • Polypeptides of nonpolyribosomal messenger ribonucleoprotein complexes of sea urchin eggs.

    abstract::RNA competent in directing protein synthesis is sequestered in unfertilized sea urchin eggs as translationally quiescent, nonpolyribosomal, messenger ribonucleoprotein complexes (mRNPs). Following fertilization, these mRNPs are derepressed and actively translated, presumably due to changes in the mRNA-associated prote...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00553a029

    authors: Moon RT,Moe KD,Hille MB

    更新日期:1980-06-10 00:00:00

  • An additional methyl group at the 10-position of retinal dramatically slows down the kinetics of the rhodopsin photocascade.

    abstract::The present study focuses on ligand-protein interactions in a rhodopsin analogue generated from bovine opsin and the 10-methyl homologue of 11-cis-retinal. The analogue pigment displays a reduced alpha-band at 506 +/- 2 and a stronger beta-band at 325 nm. Remarkably, the rotational strength of these bands observed in ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972397y

    authors: DeLange F,Bovee-Geurts PH,VanOostrum J,Portier MD,Verdegem PJ,Lugtenburg J,DeGrip WJ

    更新日期:1998-02-03 00:00:00

  • Progressive development of a thrombin inhibitor binding site.

    abstract::The studies reported here were undertaken to determine whether the thrombin precursors prothrombin, prethrombin 1, prethrombin 2, and Meizo thrombin interact with the fluorescent, reversible thrombin inhibitor dansylarginine N,N-(3-ethyl-1,5-pentanediyl)amide (DAPA) [Nesheim, M. E., Prendergast, F. G., & Mann, K. G. (...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00539a003

    authors: Hibbard LS,Nesheim ME,Mann KG

    更新日期:1982-05-11 00:00:00

  • Protected sulfur transfer reactions by the Escherichia coli Suf system.

    abstract::The first step in sulfur mobilization for the biosynthesis of Fe-S clusters under oxidative stress and iron starvation in Escherichia coli involves a cysteine desulfurase SufS. Its catalytic reactivity is dependent on the presence of a sulfur acceptor protein, SufE, which acts as the preferred substrate for this enzym...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi4001479

    authors: Selbach BP,Pradhan PK,Dos Santos PC

    更新日期:2013-06-11 00:00:00

  • Low-temperature solid-state 13C NMR studies of the retinal chromophore in rhodopsin.

    abstract::Magic angle sample spinning (MASS) 13C NMR spectra have been obtained of bovine rhodopsin regenerated with retinal prosthetic groups isotopically enriched with 13C at C-5 and C-14. In order to observe the 13C retinal chromophore resonances, it was necessary to employ low temperatures (-15-----35 degrees C) to restrict...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00380a018

    authors: Smith SO,Palings I,Copié V,Raleigh DP,Courtin J,Pardoen JA,Lugtenburg J,Mathies RA,Griffin RG

    更新日期:1987-03-24 00:00:00

  • A Novel Soluble Peptide with pH-Responsive Membrane Insertion.

    abstract::Several diseases, such as cancer, are characterized by acidification of the extracellular environment. Acidosis can be employed as a target to specifically direct therapies to the diseased tissue. We have used first principles to design an acidity-triggered rational membrane (ATRAM) peptide with high solubility in sol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00856

    authors: Nguyen VP,Alves DS,Scott HL,Davis FL,Barrera FN

    更新日期:2015-11-03 00:00:00

  • Fluorescence spectroscopic studies of pressure effects on Na+,K(+)-ATPase reconstituted into phospholipid bilayers and model raft mixtures.

    abstract::To contribute to the understanding of membrane protein function upon application of pressure as relevant for understanding, for example, the physiology of deep sea organisms or for baroenzymological biotechnical processes, we investigated the influence of hydrostatic pressure on the activity of Na+,K+-ATPase enriched ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi062235e

    authors: Powalska E,Janosch S,Kinne-Saffran E,Kinne RK,Fontes CF,Mignaco JA,Winter R

    更新日期:2007-02-13 00:00:00

  • Ion Channel Formation by Tau Protein: Implications for Alzheimer's Disease and Tauopathies.

    abstract::Tau is a microtubule associated protein implicated in the pathogenesis of several neurodegenerative diseases. Because of the channel forming properties of other amyloid peptides, we employed planar lipid bilayers and atomic force microscopy to test tau for its ability to form ion permeable channels. Our results demons...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00988

    authors: Patel N,Ramachandran S,Azimov R,Kagan BL,Lal R

    更新日期:2015-12-22 00:00:00

  • Multiple metal binding domains enhance the Zn(II) selectivity of the divalent metal ion transporter AztA.

    abstract::Transition metal-transporting P1B-type CPx ATPases play crucial roles in mediating metal homeostasis and resistance in all cells. The degree to which N-terminal metal binding domains (MBDs) confer metal specificity to the transporter is unclear. We show that the two MBDs of the Zn/Cd/Pb effluxing pump Anabaena AztA ar...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi7006367

    authors: Liu T,Reyes-Caballero H,Li C,Scott RA,Giedroc DP

    更新日期:2007-10-02 00:00:00

  • A bacterially expressed mineralocorticoid receptor is associated in vitro with the 90-kilodalton heat shock protein and shows typical hormone- and DNA-binding characteristics.

    abstract::A recombinant system was developed for generation of steroid-receptor complexes in vitro. The DNA- and steroid-binding domains of the rat mineralocorticoid receptor were expressed in Escherichia coli as a fusion protein with glutathione S-transferase. The identity of the expressed recombinant protein was confirmed by ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00084a028

    authors: Caamaño CA,Morano MI,Patel PD,Watson SJ,Akil H

    更新日期:1993-08-24 00:00:00

  • Transient formation of a neutral ubisemiquinone radical and subsequent intramolecular electron transfer to pyrroloquinoline quinone in the Escherichia coli membrane-integrated glucose dehydrogenase.

    abstract::The membrane-bound quinoprotein glucose dehydrogenase (mGDH) in Escherichia coli contains pyrroloquinoline quinone (PQQ) and participates in the direct oxidation of D-glucose to D-gluconate by transferring electrons to ubiquinone (UQ). To elucidate the mechanism of ubiquinone reduction by mGDH, we applied a pulse radi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051347n

    authors: Kobayashi K,Mustafa G,Tagawa S,Yamada M

    更新日期:2005-10-18 00:00:00

  • Properties of Paracoccus denitrificans amicyanin.

    abstract::Paracoccus denitrificans synthesizes an inducible, periplasmic, blue copper protein [Husain, M., & Davidson, V.L. (1985) J. Biol. Chem. 260, 14626-14629] that can be classified as an amicyanin on the basis of its ability to accept electrons from methylamine dehydrogenase. The amino acid composition and sequence of the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00357a020

    authors: Husain M,Davidson VL,Smith AJ

    更新日期:1986-05-06 00:00:00

  • Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine.

    abstract::Purine riboswitches are RNA regulatory elements that control purine metabolism in response to intracellular concentrations of the purine ligands. Conformational changes of the guanine riboswitch aptamer domain induced by guanine binding lead to transcriptional regulation of genes involved in guanine biosynthesis. The ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9019912

    authors: Brenner MD,Scanlan MS,Nahas MK,Ha T,Silverman SK

    更新日期:2010-03-02 00:00:00

  • Nucleotide sequence of the gene for the gamma chain of human fibrinogen.

    abstract::A human genomic DNA library was screened for the gene coding for the gamma chain of fibrinogen by using a human cDNA for the gamma chain as a hybridization probe. The gene was identified in three overlapping recombinant lambda bacteriophage, and its sequence, including the immediate 5' and 3' flanking regions, was det...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00329a041

    authors: Rixon MW,Chung DW,Davie EW

    更新日期:1985-04-09 00:00:00

  • A large solvent isotope effect on protein association thermodynamics.

    abstract::Solvent reorganization can contribute significantly to the energetics of protein-protein interactions. However, our knowledge of the magnitude of the energetic contribution is limited, in part, by a dearth of quantitative experimental measurements. The biotin repressor forms a homodimer as a prerequisite to DNA bindin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi400952m

    authors: Eginton C,Beckett D

    更新日期:2013-09-24 00:00:00

  • Substrate binding to the peripheral site of acetylcholinesterase initiates enzymatic catalysis. Substrate inhibition arises as a secondary effect.

    abstract::Two sites of ligand interaction in acetylcholinesterase (AChE) were first demonstrated in ligand binding studies and later confirmed by crystallography, site-specific mutagenesis, and molecular modeling: an acylation site at the base of the active site gorge and a peripheral site at its mouth. We recently introduced a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9813577

    authors: Szegletes T,Mallender WD,Thomas PJ,Rosenberry TL

    更新日期:1999-01-05 00:00:00

  • Side-chain dynamics of two aromatic amino acids in pancreatic phospholipase A2 as studied by deuterium nuclear magnetic resonance.

    abstract::The flexibility of individual amino acid side chains of pancreatic phospholipase A2 in aqueous and micellar solutions was studied with deuterium nuclear magnetic resonance (2H NMR). Bovine pancreatic phospholipase A2 was selectively deuterated at the aromatic ring systems of Trp-3 and Phe-5 and porcine pancreatic phos...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00334a029

    authors: Allegrini PR,van Scharrenburg GJ,Slotboom AJ,de Haas GH,Seelig J

    更新日期:1985-06-18 00:00:00

  • Structure and mutational analysis of the PhoN protein of Salmonella typhimurium provide insight into mechanistic details.

    abstract::The Salmonella typhimurium PhoN protein is a nonspecific acid phosphatase and belongs to the phosphatidic acid phosphatase type 2 (PAP2) superfamily. We report here the crystal structures of phosphate-bound PhoN, the PhoN-tungstate complex, and the T159D mutant of PhoN along with functional characterization of three m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi062180g

    authors: Makde RD,Mahajan SK,Kumar V

    更新日期:2007-02-27 00:00:00

  • Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene.

    abstract::The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determine the mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarily cis-syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotational and translational settings of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991771m

    authors: Liu X,Mann DB,Suquet C,Springer DL,Smerdon MJ

    更新日期:2000-01-25 00:00:00

  • Fluoride inhibition of Klebsiella aerogenes urease: mechanistic implications of a pseudo-uncompetitive, slow-binding inhibitor.

    abstract::Klebsiella aerogenes urease uses a dinuclear nickel active site to catalyze the hydrolysis of urea. Here, we describe the steady-state and pre-steady-state kinetics of urease inhibition by fluoride. Urease is slowly inhibited by fluoride in both the presence and absence of substrate. Steady-state rate studies yield pa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi992287m

    authors: Todd MJ,Hausinger RP

    更新日期:2000-05-09 00:00:00

  • Threonine inhibition of the aspartokinase--homoserine dehydrogenase I of Escherichia coli. Threonine binding studies.

    abstract::Both activities of the aspartokinase--homoserine I (AK-HSD) of Escherichia coli are inhibited by threonine. Careful threonine binding studies have now been done which have allowed us to distinguish the various effects of threonine on the enzyme. The ultrafiltration technique of H. Paulus ((1969) Anal. Biochem. 32, 101...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00610a014

    authors: Bearer CF,Neet KE

    更新日期:1978-08-22 00:00:00

  • Conformational fluctuation of native-like and molten-globule-like cytochrome c observed by time-resolved hole burning.

    abstract::Nanosecond to millisecond conformational fluctuations of Zn-substituted cytochrome c (ZnCytc) have been studied by the time-resolved transient hole-burning method. The investigation of low-temperature dynamics has been made on the ZnCytc solution sample in a water-glycerol mixture. The conformational fluctuations in t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981568b

    authors: Shibata Y,Takahashi H,Kaneko R,Kurita A,Kushida T

    更新日期:1999-02-09 00:00:00

  • Sequence of a cDNA clone encoding the zinc metalloproteinase hemorrhagic toxin e from Crotalus atrox: evidence for signal, zymogen, and disintegrin-like structures.

    abstract::The sequence of two overlapping cDNA clones for the zinc metalloproteinase hemorrhagic toxin e (also known as atrolysin e, EC 3.4.24.44) from the venom gland of Crotalus atrox, the Western diamondback rattlesnake, is presented. The assembled cDNA sequence is 1975 nucleotides in length and encodes an open reading frame...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00142a005

    authors: Hite LA,Shannon JD,Bjarnason JB,Fox JW

    更新日期:1992-07-14 00:00:00

  • A new bifunctional spin-label suitable for saturation-transfer EPR studies of protein rotational motion.

    abstract::A new bifunctional spin-label (BSL) has been synthesized that can be immobilized on the surface of proteins, allowing measurement of rotational motion of proteins by saturation-transfer electron paramagnetic resonance (STEPR). The spin-label contains a photoactivatable azido moiety, a cleavable disulfide, and a nitrox...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00476a014

    authors: Wilcox MD,Parce JW,Thomas MJ,Lyles DS

    更新日期:1990-06-19 00:00:00