Volumetric and spectroscopic characterizations of the native and acid-induced denatured states of staphylococcal nuclease 1 1Edited by P. E. Wight

Filfil, Rana; Chalikian, Tigran V.

doi:10.1006/jmbi.2000.3773

Cited by 42 publications

(43 citation statements)

References 77 publications

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“…These results are briefly explained according to the changes in cavities and hydration below; more-detailed discussions are available elsewhere (Taulier and Chalikian 2002;Chalikian 2003). Tamura and Gekko (1995), c Kamiyama and Gekko (1997), d Gekko et al (2003), e Filfil and Chalikian (2000), f Chalikian et al (1995), g Kamiyama et al (1999), h Chalikian et al (1997) (Tamura and Gekko 1995;Kamiyama and Gekko 1997). Theseˇs o values are close to the average for unfolded proteins estimated from those of amino acid residues (Lee et al 2008).…”

Section: Volume and Compressibility Changes Due To Conformational Tramentioning

confidence: 78%

Volume and Compressibility of Proteins

Gekko

2015

Subcellular Biochemistry

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The partial specific (or molar) volume, expansibility, and compressibility of a protein are fundamental thermodynamic quantities for characterizing its structure in solution. We review the definitions, measurements, and implications of these volumetric quantities in relation to protein structural biology. The partial specific volumes under constant molality (isomolal) and chemical potential (isopotential) conditions of the cosolvent (multicomponent systems) are explained in terms of preferential solvent interactions relevant to the solubility and stability of proteins. The partial expansibility is briefly discussed in terms of the effects of temperature on protein-solvent interactions (hydration) and internal packing defects (cavities). We discuss the compressibility-structure-function relationships of proteins based on analyses of the correlations between the partial adiabatic compressibilities and the structures or functions of various globular proteins (including mutants), focusing on the roles of the internal cavities in structural fluctuations. The volume and compressibility changes associated with various conformational transitions are also discussed in terms of the changes in hydration and cavities in order to elucidate the nonnative structures and the transition mechanisms, especially those associated with pressure denaturation.

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Section: Volume and Compressibility Changes Due To Conformational Tramentioning

confidence: 78%

Volume and Compressibility of Proteins

Gekko

2015

Subcellular Biochemistry

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“…(1) and previously described protocols to calculate the pH-dependent protonation contributions to changes in relative molar sound velocity increment, D[u], and volume, Dv. 51,52 In these calculations, we used the values of D[U] i and DV i that have been determined from investigating low molecular weight model compounds. 51,52 In addition, changes in relative specific sound velocity increment, D[u], generally include the relaxation contribution.…”

Section: Resultsmentioning

confidence: 99%

“…51,52 In these calculations, we used the values of D[U] i and DV i that have been determined from investigating low molecular weight model compounds. 51,52 In addition, changes in relative specific sound velocity increment, D[u], generally include the relaxation contribution. This contribution results from proton transfer reactions accompanying protonation/ deprotonation of titrable amino acids, which also cause a relaxation increase in ultrasonic absorption.…”

Section: Resultsmentioning

confidence: 99%

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Compressibility changes accompanying conformational transitions of apomyoglobin

2005

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We used high-precision density and ultrasonic velocity measurements to characterize the native (N), molten globule (MG), and unfolded (U) conformations of apomyoglobin. The molten globule states that were studied in this work include the MG(pH4)(NaCl) state observed at pH 4 and 20 mM NaCl, the MG(pH4)(NaTCA) state observed at pH 4 and 20 mM sodium trichloracetate (NaTCA), the MG(pH2)(NaCl) state observed at pH 2 and 200 mM NaCl, and the MG(pH2)(NaTCA) state observed at pH 2 and 20 mM NaTCA. We used our densimetric and acoustic data to evaluate changes in adiabatic compressibility associated with the acid- or salt-induced N-to-MG, MG-to-U, MG-to-MG, and U-to-MG transitions of the protein. The N-to-MG(pH4)(NaCl) and N-to-MG(pH4)(NaTCA) transitions are accompanied by decreases in compressibility of -(3.0 +/- 0.6) x 10(-6) and -(2.0 +/- 0.6) x 10(-6) cm3 g(-1)bar(-1), respectively. The N-to-MG(pH2)(NaCl) and N-to-MG(pH2)(NaTCA) transitions are associated with compressibility changes of -(4.9 +/- 1.1) x 10(-6) and (0.7 +/- 0.9) x 10(-6) cm3 g(-1) bar(-1), respectively. We interpret these data in terms of the degree of unfolding of the various molten globule forms of apomyoglobin. In general, our compressibility data reveal significant disparities between the various equilibrium molten globule states of apomyoglobin while also quantitatively characterizing each of these states. Volumetric insights provided by our data facilitate gaining a better understanding of the folding pathways, intermediates, and kinetics of apomyoglobin folding.

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“…Acoustic titration-like experiments were also made in order to characterize the acid-induced denaturation of staphylococcal nuclease at different urea concentrations, 13 to study the binding of the cationic surfactant dodecyltrimethylammonium bromide to short fragments of DNA in dilute solutions at 1 mM NaCl, 14 to analyze the binding of alamethicin to unilamellar DMPC vesicles, 15 and also to study interactions of Co(NH3)6 3+ with calf thymus DNA 16 and Cs + and Mg 2+ with polynucleotides. 17 All of the above listed reports encouraged us to test if sound speed or density measurements can be applied for monitoring simple reactions, like acid-base titration, and how to describe the observed changes.…”

Section: Introductionmentioning

confidence: 99%

Ultrasonic and Densimetric Titration Applied for Acid-base Reactions

Burakowski

Gliński

2014

ANAL. SCI.

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Classical acoustic acid-base titration was monitored using sound speed and density measurements. Plots of these parameters, as well as of the adiabatic compressibility coefficient calculated from them, exhibit changes with the volume of added titrant. Compressibility changes can be explained and quantitatively predicted theoretically in terms of Pasynski theory of non-compressible hydrates combined with that of the additivity of the hydration numbers with the amount and type of ions and molecules present in solution. It also seems that this development could be applied in chemical engineering for monitoring the course of chemical processes, since the applied experimental methods can be carried out almost independently on the medium under test (harmful, aggressive, etc.).

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Volumetric and spectroscopic characterizations of the native and acid-induced denatured states of staphylococcal nuclease 1 1Edited by P. E. Wight

Cited by 42 publications

References 77 publications

Volume and Compressibility of Proteins

Volume and Compressibility of Proteins

Compressibility changes accompanying conformational transitions of apomyoglobin

Ultrasonic and Densimetric Titration Applied for Acid-base Reactions

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