[3] Hydrogen—Tritium exchange

Englander, S. W.; Englander, Joan J.

doi:10.1016/s0076-6879(78)49005-6

Cited by 83 publications

(47 citation statements)

References 41 publications

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“…polypeptide sequence, peptide amide hydrogens are always maximally accessible to water and exchange at their maximal rate, which is approximately (within a factor of 30) the same for all amides; their half-life of exchange is in the range of 1 sec at 0°C and pH 7.0 (41,42). Most amide hydrogens in structured peptides or proteins exchange much more slowly (up to 10 9 -fold reduction), reflecting the fact that exchange occurs only when transient unfolding fluctuations fully expose the amides to solvent water.…”

mentioning

confidence: 86%

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Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS

Pantazatos

Kim

Klock

et al. 2004

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

142

109

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Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen͞high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner.

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confidence: 86%

“…The chemical mechanisms of the exchange reactions are understood, and several well defined factors can profoundly alter exchange rates (12,(39)(40)(41). One of these factors is the extent to which a particular exchangeable hydrogen is exposed (accessible) to water.…”

mentioning

confidence: 99%

Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS

Pantazatos

Kim

Klock

et al. 2004

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

142

109

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“…9 -12 However, the smooth, continuous deformations of the helix implied by the elastic model are inadequate to explain some observations. For example, the ability of the hydrogen-bonded ring protons of the bases in DNA to exchange at temperatures well below the denaturation point 13 suggests that the double helix contains a small number of unpaired bases at room temperature. Torsional fluctuations that lead to a transient local unwinding of the helix are also thought to be involved in many important biological events.…”

Section: Introductionmentioning

confidence: 99%

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Millar

Robbins

Zewail

1982

The Journal of Chemical Physics

159

109

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Subnanosecond time-resolved fluorescence depolarization has been used to monitor the reorientation of ethidium bromide intercalated in native DNA, synthetic polynucleotide complexes, and in supercoiled plasmid DNA. The fluorescence polarization anisotropy was successfully analyzed with an elastic model of DNA dynamics, including both torsion and bending, which yielded an accurate value for the torsional rigidity of the different DNA samples. The dependence of the torsional rigidity on the base sequence, helical structure, and tertiary structure was experimentally observed. The magnitude of the polyelectrolyte contribution to the torsional rigidity of DNA was measured over a wide range of ionic strength, and compared with polyelectrolyte theories for the persistence length. We also observed a rapid initial reorientation of the intercalated ethidium which had a much smaller amplitude in RNA than in DNA.

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“…1 and 2; for review see ref. 3) and remote from any denaturation transitions. High molecular weight DNA, for example, exchanges its hydrogens at 0C with a half-time of 5 min in solvent and salt conditions such that its thermal denaturation temperature is above 80'C (4).…”

mentioning

confidence: 99%

“…x-r p(x) = o o f(r,s) dr ds [8] [3] in which AS, is the entropy and AfHS the enthalpy of formation of an open segment, R is the gas constant, and T is absolute temperature (13). Because, by hypothesis, each segment contains (L/i) open base pairs and the mean of the excursion is x = f1 -p(x)ldx.…”

mentioning

confidence: 99%

Nature of the open state in long polynucleotide double helices: possibility of soliton excitations.

Englander¹,

Kallenbach²,

Heeger³

et al. 1980

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

450

184

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The existence of transiently open states in DNA and synthetic polynucleotide double helices as been demonstrated by hydrogen exchange measurements; base pairs reversibly separate and reclose, exposing nucleotide protons to exchange with solvent protons. Recently it has been possible to define the equilibrium kinetic, and activation parameters of the major open state tdat determines base pair hydrogen exchange. However, there is no direct information at the moment about the conformation of the open form. Here we consider the possibility that the low energy and slow opening and closing rates observed reflect a deformation involving several adjacent base pairs. Assuming a mobile open unit capable of diffusing along the double helix, we find that available data are consistent with structures of 10 or so adjacent open pairs. It is further suggested that these structures correspond to thermally induced so on excitations of the double helix, which retain coherence by sharing the energy of a twist deformation among several base tairs. Solitons

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[3] Hydrogen—Tritium exchange

Cited by 83 publications

References 41 publications

Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS

Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Nature of the open state in long polynucleotide double helices: possibility of soliton excitations.

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