Folding energetics of ligand binding proteins. I. Theoretical model.

Abstract:

:Heat capacity curves as obtained from differential scanning calorimetry are an outstanding source for molecular information on protein folding and ligand-binding energetics. However, deconvolution of C(p) data of proteins in the presence of ligands can be compromised by indeterminacies concerning the correct choice of the statistical thermodynamic ensemble. By convent, the assumption of constant free ligand concentration has been used to derive formulae for the enthalpy. Unless the ligand occurs at large excess, this assumption is incorrect. Still the relevant ensemble is the grand canonical ensemble. We derive formulae for both constraints, constancy of total or free ligand concentration and illustrate the equations by application to the typical equilibrium Nx <=> N + x <=> D + x. It is demonstrated that as long as the thermodynamic properties of the ligand can be completely corrected for by performing a reference measurement, the grand canonical approach provides the proper and mathematically significantly simpler choice. We demonstrate on the two cases of sequential or independent ligand-binding the fact, that similar binding mechanisms result in different and distinguishable heat capacity equations. Finally, we propose adequate strategies for DSC experiments as well as for obtaining first estimates of the characteristic thermodynamic parameters, which can be used as starting values in a global fit of DSC data.

journal_name

J Mol Biol

authors

Rösgen J,Hinz HJ

doi

10.1006/jmbi.2000.4359

keywords:

subject

Has Abstract

pub_date

2001-03-02 00:00:00

pages

809-24

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94359-6

journal_volume

306

pub_type

杂志文章
  • Trypanosoma brucei 5'ETS A'-cleavage is directed by 3'-adjacent sequences, but not two U3 snoRNA-binding elements, which are all required for subsequent pre-small subunit rRNA processing events.

    abstract::Trypanosoma brucei pre-rRNA processing commences by cleavage near the 5' end of 5.8 S sequences. The 5' external transcribed spacer (5'ETS) is removed from pre-small subunit (SSU) rRNAs by sequential cleavages at internal A' and A0 sites, and A1 at the 5' end of SSU rRNA. The A' and A0 sites positionally resemble the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5078

    authors: Hartshorne T,Toyofuku W,Hollenbaugh J

    更新日期:2001-11-02 00:00:00

  • Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

    abstract::The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90134-6

    authors: Kostrewa D,Granzin J,Stock D,Choe HW,Labahn J,Saenger W

    更新日期:1992-07-05 00:00:00

  • Functional structures of the recA protein found by chimera analysis.

    abstract::We developed a novel genetic method for finding functional regions of a protein by the analysis of chimeras formed between homologous proteins. Sets of chimeric genes were made by intramolecular homologous recombination in a linearized plasmid DNA carrying both recA genes of Escherichia coli and Pseudomonas aeruginosa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90622-q

    authors: Ogawa T,Shinohara A,Ogawa H,Tomizawa J

    更新日期:1992-08-05 00:00:00

  • Long range base-pairing in the leftward transcription unit of bacteriophage lambda. Characterization by electron microscopy and computer-aided sequence analysis.

    abstract::Restriction fragments of bacteriophage lambda DNA corresponding to the major leftward transcription unit were purified, denatured to form single-stranded DNA, self-annealed, and examined by electron microscopy. Three intrastrand stem and loop secondary structures were observed reproducibly and the locations of the pai...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90070-6

    authors: Edlind TD,Cooley TE,Richards SH,Ihler GM

    更新日期:1984-11-05 00:00:00

  • Limited proteolysis unmasks specific DNA-binding of the murine RNA polymerase I-specific transcription termination factor TTFI.

    abstract::Previously we have shown that nuclear extracts from mouse cells contain a heterogeneous group of polypeptides (p65, p80, p90, p100) which form distinct DNA-protein complexes on the 18 base-pair sequence element (termed Sal-box), which constitutes the murine rDNA transcription termination signal. These distinct protein...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90213-4

    authors: Smid A,Finsterer M,Grummt I

    更新日期:1992-10-05 00:00:00

  • Molecular evolution of antibody affinity for sensitive detection of botulinum neurotoxin type A.

    abstract::Botulism is caused by botulinum neurotoxin (BoNT), the most poisonous substance known. Potential use of BoNT as a biothreat agent has made development of sensitive assays for toxin detection and potent antitoxin for treatment of intoxication a high priority. To improve detection and treatment of botulism, molecular ev...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.003

    authors: Razai A,Garcia-Rodriguez C,Lou J,Geren IN,Forsyth CM,Robles Y,Tsai R,Smith TJ,Smith LA,Siegel RW,Feldhaus M,Marks JD

    更新日期:2005-08-05 00:00:00

  • An in-the-groove view of DNA structures in complexes with proteins.

    abstract::DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groov...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0055

    authors: Suzuki M,Yagi N

    更新日期:1996-02-09 00:00:00

  • Crystal structure of the catalytic subunit of Cdc25B required for G2/M phase transition of the cell cycle.

    abstract::Cdc25B is a dual specificity phosphatase involved in the control of cyclin-dependent kinases and the progression of cells through the cell cycle. A series of minimal domain Cdc25B constructs maintaining catalytic activity have been expressed. The structure of a minimum domain construct binding sulfate was determined a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3168

    authors: Reynolds RA,Yem AW,Wolfe CL,Deibel MR Jr,Chidester CG,Watenpaugh KD

    更新日期:1999-10-29 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

  • Molecular basis for mutation in a surface protein expressed by malaria parasites.

    abstract::Plasmodium knowlesi parasites isolated from a rhesus monkey vaccinated with a 143,000/140,000 Mr merozoite surface protein no longer expressed this protein. To study the molecular basis for the mutations, a lambda gt11 cDNA expression library constructed from the original parasite clone was screened with rabbit antise...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90204-5

    authors: Hudson DE,Wellems TE,Miller LH

    更新日期:1988-10-05 00:00:00

  • Deletion analysis of the lambda tR1 termination region. Effect of sequences near the transcript release sites, and the minimum length of rho-dependent transcripts.

    abstract::In order to determine how much of the natural sequence is required for function of the lambda tR1 rho-dependent terminator, and to determine the minimum length required, we made two deletion series of a tR1 derivative that contains mostly foreign DNA, encoding C-rich RNA, substituted for the natural upstream sequences...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1229

    authors: Hart CM,Roberts JW

    更新日期:1994-04-01 00:00:00

  • Optogenetic Control of Ca2+ and Voltage-Dependent Large Conductance (BK) Potassium Channels.

    abstract::Ca2+ concentration jumps for the activation of Ca2+-dependent ion channels or transporters can be obtained either by fast solution exchange or by the use of caged Ca2+. Here, we report on an alternate optogenetic method for the activation of Ca2+ and voltage-dependent large conductance (BK) potassium channels. This wa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.02.004

    authors: Mager T,Wood PG,Bamberg E

    更新日期:2017-03-24 00:00:00

  • Three members of the human pyruvate dehydrogenase kinase gene family are direct targets of the peroxisome proliferator-activated receptor beta/delta.

    abstract::The nuclear receptors peroxisome proliferator-activated receptors (PPARs) are known for their critical role in the metabolic syndrome. Here, we show that they are direct regulators of the family of pyruvate dehydrogenase kinase (PDK) genes, whose products act as metabolic homeostats in sensing hunger and satiety level...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.06.091

    authors: Degenhardt T,Saramäki A,Malinen M,Rieck M,Väisänen S,Huotari A,Herzig KH,Müller R,Carlberg C

    更新日期:2007-09-14 00:00:00

  • Solution structure by NMR of circulin A: a macrocyclic knotted peptide having anti-HIV activity.

    abstract::The three-dimensional solution structure of circulin A, a 30 residue polypeptide from the African plant Chassalia parvifolia, has been determined using two-dimensional 1H-NMR spectroscopy. Circulin A was originally identified based upon its inhibition of the cytopathic effects and replication of the human immunodefici...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2276

    authors: Daly NL,Koltay A,Gustafson KR,Boyd MR,Casas-Finet JR,Craik DJ

    更新日期:1999-01-08 00:00:00

  • Native-like partially folded conformations and folding process revealed in the N-terminal large fragments of staphylococcal nuclease: a study by NMR spectroscopy.

    abstract::The N-terminal large fragments of staphylococcal nuclease (SNase), SNase110 (1-110 residues), SNase121 (1-121 residues), and SNase135 (1-135 residues), and the fragment mutants G88W110, G88W121, V66W110 and V66W121 were studied by heteronuclear multidimensional NMR spectroscopy. Ensembles of co-existent native-like pa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00660-0

    authors: Feng Y,Liu D,Wang J

    更新日期:2003-07-18 00:00:00

  • Supramolecular Assembly of Human Pulmonary Surfactant Protein SP-D.

    abstract::Pulmonary surfactant protein D (SP-D) is a glycoprotein from the collectin family that is a component of the lung surfactant system. It exhibits host defense and immune regulatory functions in addition to contributing to the homeostasis of the surfactant pool within the alveolar airspaces. It is known that the SP-D mo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.03.027

    authors: Arroyo R,Martín-González A,Echaide M,Jain A,Brondyk WH,Rosenbaum J,Moreno-Herrero F,Pérez-Gil J

    更新日期:2018-05-11 00:00:00

  • Refined structure of spinach glycolate oxidase at 2 A resolution.

    abstract::The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 inde...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90178-2

    authors: Lindqvist Y

    更新日期:1989-09-05 00:00:00

  • Molecular architecture and structural transitions of a Clostridium thermocellum mini-cellulosome.

    abstract::The cellulosome is a highly elaborate cell-bound multienzyme complex that efficiently orchestrates the deconstruction of cellulose and hemicellulose, two of the nature's most abundant polymers. Understanding the intricacy of these nanomachines evolved by anaerobic microbes could sustain the development of an effective...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.01.060

    authors: García-Alvarez B,Melero R,Dias FM,Prates JA,Fontes CM,Smith SP,Romão MJ,Carvalho AL,Llorca O

    更新日期:2011-04-08 00:00:00

  • Crystallization of transmembrane proteins in cubo: mechanisms of crystal growth and defect formation.

    abstract::Crystallization of membrane proteins is a major stumbling block en route to elucidating their structure and understanding their function. The novel concept of membrane protein crystallization from lipidic cubic phases, "in cubo", has yielded well-ordered crystals and high-resolution structures of several membrane prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.09.022

    authors: Qutub Y,Reviakine I,Maxwell C,Navarro J,Landau EM,Vekilov PG

    更新日期:2004-11-05 00:00:00

  • M-LDH serves as a regulatory subunit of the cytosolic substrate-channelling complex in vivo.

    abstract::Nucleoside diphosphate kinase A (NDPK-A) regulates the alpha1 isoform of the AMP-activated protein kinase (AMPK alpha1) selectively, independent of [AMP] and surrounding [ATP], by a process termed substrate channelling. Here, we show, using a range of empirically validated biochemical techniques, that the muscle form ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.05.081

    authors: Jovanović S,Jovanović A,Crawford RM

    更新日期:2007-08-10 00:00:00

  • The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences.

    abstract::The papillomavirus E2 transcription and replication factors bind to the DNA consensus ACCGN(4)CGGT sequence (E2-BS), through both direct and indirect readout mechanisms. The two symmetric half-sites ACCG.CGGT are highly conserved in the genomes and are hydrogen bound with E2. Although E2 does not contact the N4 spacer...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.078

    authors: Djuranovic D,Oguey C,Hartmann B

    更新日期:2004-06-11 00:00:00

  • The preprotein translocase of the inner mitochondrial membrane: evolutionary conservation of targeting and assembly of Tim17.

    abstract::The preprotein translocase of the inner mitochondrial membrane has only been described in Saccharomyces cerevisiae to date. We report that the essential subunit Tim17 is highly conserved in evolution. The targeting and assembly of yeast Tim17 as well as that of human and Drosophila melanogaster Tim17 were characterize...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0522

    authors: Bömer U,Rassow J,Zufall N,Pfanner N,Meijer M,Maarse AC

    更新日期:1996-10-04 00:00:00

  • Myosin isoform determines the conformational dynamics and cooperativity of actin filaments in the strongly bound actomyosin complex.

    abstract::We used transient phosphorescence anisotropy to detect the microsecond rotational dynamics of erythrosin-iodoacetamide-labeled actin strongly bound to single-headed fragments of muscle myosin subfragment 1 (S1) and non-muscle myosin V (MV). The conformational dynamics of actin filaments in solution are markedly influe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.063

    authors: Prochniewicz E,Chin HF,Henn A,Hannemann DE,Olivares AO,Thomas DD,De La Cruz EM

    更新日期:2010-02-26 00:00:00

  • Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.

    abstract::The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resoluti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2628

    authors: Song SY,Xu YB,Lin ZJ,Tsou CL

    更新日期:1999-04-09 00:00:00

  • Static disorder and librational motions of the purine bases in films of oriented Li-DNA.

    abstract::Solid-state 2H nuclear magnetic resonance line shapes have been obtained from folded films of oriented Li-DNA molecules with the purine bases selectively labeled with deuterium at the 8-position. From line shape simulations, the static base tilts as well as the anisotropic motional amplitudes were determined as a func...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90461-5

    authors: Brandes R,Vold RR,Kearns DR,Rupprecht A

    更新日期:1988-07-20 00:00:00

  • The rabbit C family of short, interspersed repeats. Nucleotide sequence determination and transcriptional analysis.

    abstract::The C repeat family was first observed in the rabbit beta-like gene family. We have estimated the repetition frequency of the C repeats, determined the nucleotide sequence of three intact members and one truncated member, and have investigated the size, tissue specificity, and intracellular localization of C repeat tr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90379-6

    authors: Cheng JF,Printz R,Callaghan T,Shuey D,Hardison RC

    更新日期:1984-06-15 00:00:00

  • Involvement of the C-terminal region of yeast proteinase B inhibitor 2 in its inhibitory action.

    abstract::Yeast proteinase B inhibitor 2 (YIB2), which is composed of 74 amino acid residues, is an unusual serine protease inhibitor, since it lacks disulfide bonds. To identify its reactive site for proteases, we constructed an expression system for a synthetic YIB2 gene and then attempted to change the inhibitory properties ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2498

    authors: Kojima S,Deguchi M,Miura K

    更新日期:1999-02-26 00:00:00

  • Improving profile HMM discrimination by adapting transition probabilities.

    abstract::Profile hidden Markov models (HMMs) are used to model protein families and for detecting evolutionary relationships between proteins. Such a profile HMM is typically constructed from a multiple alignment of a set of related sequences. Transition probability parameters in an HMM are used to model insertions and deletio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.023

    authors: Wistrand M,Sonnhammer EL

    更新日期:2004-05-07 00:00:00

  • A novel allosteric mechanism in haemoglobin. Structure of bovine deoxyhaemoglobin, absence of specific chloride-binding sites and origin of the chloride-linked Bohr effect in bovine and human haemoglobin.

    abstract::The structure of bovine deoxyhaemoglobin has been determined at 2.2 A resolution and refined to an R-factor of 0.193 for all 32,583 reflections, and a free R-factor of 0.249 for 1527 reflections excluded from the refinement. The structure shows no significant differences between the alpha-carbon positions of bovine an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1530

    authors: Perutz MF,Fermi G,Poyart C,Pagnier J,Kister J

    更新日期:1993-10-05 00:00:00

  • Specific heteromeric association of four transmembrane peptides derived from platelet glycoprotein Ib-IX complex.

    abstract::As the receptor on the platelet surface for von Willebrand factor, glycoprotein (GP) Ib-IX complex is critically involved in hemostasis and thrombosis. How the complex is assembled from GP Ibalpha, GP Ib beta and GP IX subunits, all of which are type I transmembrane proteins, is not entirely clear. Genetic and mutatio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.037

    authors: Luo SZ,Li R

    更新日期:2008-10-03 00:00:00