Volumetric Characterizations of the Native, Molten Globule and Unfolded States of Cytochromecat Acidic pH

Chalikian, Tigran V.; Gindikin, Vera; Breslauer, Kenneth J.

doi:10.1006/jmbi.1995.0377

Cited by 129 publications

(128 citation statements)

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“…Consistent with this expectation, we find the acid-induced N-to-MG transition of cytochrome c to be accompanied by an -2-fold decrease in kh (9)-Furthermore, although the volume of the water-inaccessible core, VM, also should decrease upon a N-to-Cl transition, the intrinsic coefficient of adiabatic compressibility, ,BM, of the core should increase due to loosening of the interior packing. Consistent with this expectation, we find the acid-induced N-to-MG transition of cytochrome c to be accompanied by a 4.5-fold increase in ,BM (9). As we have shown for cytochrome c (9), this increase in ,BM prevails over the decrease in VM, thereby resulting in a net increase in the intrinsic contribution, kM, to the partial compressibility (see Eq.…”

supporting

confidence: 88%

“…Consistent with this expectation, we find the acid-induced N-to-MG transition of cytochrome c to be accompanied by a 4.5-fold increase in ,BM (9). As we have shown for cytochrome c (9), this increase in ,BM prevails over the decrease in VM, thereby resulting in a net increase in the intrinsic contribution, kM, to the partial compressibility (see Eq. 2).…”

supporting

confidence: 88%

“…These Ak' values can be rationalized in terms of changes in a positively contributing intrinsic component, kM, and a negatively contributing hydration component, kh, with the latter diminishing with increasing protein hydration (ref. 8 kM increases for the N-to-Cl and N-to-PU transitions but is reduced almost to zero for the N-to-FU transition (9 compressibility, g3M, of this core being low and close to that of organic solids (7).…”

mentioning

confidence: 89%

“…For cytochrome c, we find the partial specific adiabatic compressibility, k', of the protein to vary significantly with the nature of the protein conformational state present in solution (9). The following rank order emerges: k' (CI) > ks (N) > k' (PU) > k' (FU).…”

mentioning

confidence: 90%

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Compressibility as a means to detect and characterize globular protein states.

Chalikian

Breslauer

1996

Proc. Natl. Acad. Sci. U.S.A.

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supporting

confidence: 88%

supporting

confidence: 88%

mentioning

confidence: 89%

mentioning

confidence: 90%

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Compressibility as a means to detect and characterize globular protein states.

Chalikian

Breslauer

1996

Proc. Natl. Acad. Sci. U.S.A.

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“…Ultrasonic velocimetric titrations of 3 mM poly[r(A)] with 12 mM poly[r(U)], at 20, 30, and 40°C, were performed as previously described (23)(24)(25)(26). …”

Section: Methodsmentioning

confidence: 99%

A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

Chalikian

Völker

Plum

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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We use a combination of calorimetric and volumetric techniques to detect and to characterize the thermodynamic changes that accompany helix-to-coil transitions for five polymeric nucleic acid duplexes. Our calorimetric measurements reveal that melting of the duplexes is accompanied by positive changes in heat capacity (⌬C P ) of similar magnitude, with an average ⌬C P value of 64.6 ؎ 21.4 cal deg ؊1 mol ؊1 . When this heat capacity value is used to compare significantly different transition enthalpies (⌬H o ) at a common reference temperature, T ref , we find ⌬H T ref for duplex melting to be far less dependent on duplex type, base composition, or base sequence than previously believed on the basis of the conventional assumption of a near-zero value for ⌬C P . Similarly, our densimetric and acoustic measurements reveal that, at a given temperature, all the ATand AU-containing duplexes studied here melt with nearly the same volume and compressibility changes. In the aggregate, our results, in conjunction with literature data, suggest a more unified picture for the thermodynamics of nucleic acid duplex melting. Specifically, when compared at a common temperature, the apparent large differences present in the literature for the transition enthalpies of different duplexes become much more compressed, and the melting of all-AT-and all-AU-containing duplexes exhibits similar volume and compressibility changes despite differences in sequence and conformation. Thus, insofar as thermodynamic properties are concerned, when comparing duplexes, the temperature under consideration is as important as, if not more important than, the duplex type, the base composition, or the base sequence. This general behavior has significant implications for our basic understanding of the forces that stabilize nucleic acid duplexes. This behavior also is of practical significance in connection with the use of thermodynamic databases for designing probes and for assessing the affinity and specificity associated with hybridization-based protocols used in a wide range of sequencing, diagnostic, and therapeutic applications.Thermodynamic studies of nucleic acids have produced data of both fundamental and practical importance. On the fundamental side, such studies have provided insight into the nature and strength of the forces that stabilize nucleic acids in the myriad of structural states they can assume (1-7). On the practical side, such studies have produced databases that are used to predict the stability and selectivity of hybridization events required in a broad range of nucleic acid-based diagnostic and therapeutic protocols (3, 8-11, 19, 42-44).Three aspects of the current nucleic acid thermodynamic library that are conspicuously deficient are values for the heat capacity change(s), ⌬C P , the volume changes, ⌬V, and the compressibility changes, ⌬K s , which accompany nucleic acid conformational transitions. These deficiencies are of particular concern because ⌬C P , ⌬V, and ⌬K s provide unique insights into the role of solvent i...

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